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Additional data File 1.
Supplemental Material for:
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium
purpureum.
Richard Sucgang1*, Alan Kuo2*, Xiangjun Tian3*, William Salerno1*, Anup Parikh4, Christa L.
Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris
Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6,
Christophe Anjard7, Madan Babu Mohan8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van
der Wel5, Mariko Katoh-Kurasawa 4, Christopher Dinh1, Pedro M. Coutinho9, Tamao Saito10,
Marek Elias11, Pauline Schaap12, Robert R. Kay8, Bernard Henrissat9, Ludwig Eichinger13,
Francisco Rivero14, Nicholas H. Putnam3, Christopher M. West5, William F. Loomis7, Rex L.
Chisholm6, Gad Shaulsky3,4, Joan E. Strassmann3, David C. Queller3, Adam Kuspa1,3,4, §, and
Igor V. Grigoriev2
1 – Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of
Medicine, Houston, TX 77030; 2 – Joint Genome Institute, Department of Energy, Walnut Creek CA; 3 –
Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005; 4 – Department
of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; 5 - Department of
Biochemistry & Molecular Biology, Oklahoma Center for Medical Glycobiology, University of
Oklahoma Health Sciences Center, Oklahoma City, OK 73104; 6 – dictyBase, Center for Genetic
Medicine, Northwestern University, 750 N Lake Shore Drive, Chicago, Illinois 60611; 7 - Section of Cell
and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla,
California 92093; 8 - Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK; 9 Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universities of AixMarseille I & II, 13288 Marseille, France; 10 – Department of Materials and Life Sciences, Sophia
University 7-1 Kioi-Cho, Chiyoda-Ku, Tokyo, Japan 102-8554; 11- Departments of Botany and
Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic; 12- College of
Life Sciences, University of Dundee, DD15EH Dundee, UK; 13 - Center for Molecular Medicine
Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany; 14- Centre for
Biomedical Research, The Hull York Medical School and Department of Biological Sciences, University
of Hull, Hull HU6 7RX, UK.
* Equal Contributors
§
Corresponding author
1
Description of the genome
The initial annotation of the 799 scaffolds and 33 Mbp of JGI's 8.41X assembly of the
Dictyostelium purpureum DpAX1 genome [13].
Current statistics at 8.41x coverage:
Main genome scaffold total: 799
Main genome contig total: 1213
Main genome scaffold sequence total: 33.0 MB
Main genome contig sequence total: 32.9 MB (with 0.4% as gaps)
Main genome scaffold N/L50: 156/66.9 KB
Main genome contig N/L50: 237/45.2 KB
Number of scaffolds > 50 KB: 240
% main genome in scaffolds > 50 KB: 64.9%
Prediction of protein coding genes
We predict 12410 genes, with the following average properties:
Gene length 1760.19 nt
Transcript length 1495.22 nt
Protein length 482.64 aa
Exon frequency 2.51 exons/gene
Exon length 595.25 nt
Intron length 177.26 nt
Gene density 376.4 genes/Mbp scaffold (2.66 kb/gene)
The genes were found by the following methods:
Total models: 12410 (100%)
cDNAs and ESTs: 721 (6%)
2
Similarity to nr (non-redundant): 4050 (33%)
ab initio: 7639 (62%)
The genes were validated by the following evidence:
start+stop codons: 11170 (90%)
EST support: 4039 (33%)
nr (non-redundant) hit: 11086 (89%)
Pfam hit: 6029 (49%)
Simple sequence repeats and Repetitive elements.
Many proteins of D. discoideum, including members of the ABC and histidine
kinase families, have long runs (≥ 20residues) of polyasparagine and polyglutamine.
Orthologs in D. purpureum have many fewer such runs and the ones they do have are
shorter. It appears that these and other simple sequence repeats are not essential for the
function of these proteins.
The lower abundance of simple sequence repeats, their shorter lengths, and their greater
complexity in amino acid homopolymers – are all consistent in direction with a possible bias.
The D. purpureum genome is less complete, and some simple sequence repeats could therefore
have been missed. Specifically, simple sequence repeats make assembly harder, particularly if
they fall in generally low-complexity regions. If such losses do occur, they may be most severe
for long repeats and for perfect repeats, which could explain the relative underrepresentation of
both of these kinds of repeats relative to D. discoideum. Consistent with this kind of bias, the
100-bp regions that terminate contigs in D. purpureum are enriched in repeat lengths above 10
repeats compared to sequence inside the contigs, though the difference is not large (density =
0.06 vs 0.09, p < 0.001, Mann-Whitney U test, n = 667). Any bias is unlikely to explain the
entire difference between the two species. If the two species actually had the same distributions,
it would imply that over 3/4 of the amino acid repeats were missed in D. purpureum (2645 found
versus 11243 in D. discoideum). At the upper end of the range it would imply that nearly all long
D. purpureum repeats were missed: D. discoideum has 252 repeats longer than 45 amino acids,
but D. purpureum shows only one (Supp. Fig S1b). Both of these possibilities seem very
unlikely. It is clear that D. purpureum is similar to D. discoideum in having a large amount of
simple sequence repeats and amino acid homopolymers, but is probably not as extreme.
3
Homologous amino acid homopolymers were determined by identifying aligned amino
acid repeats of the same type from global sequence alignments of pairwise orthologous proteins
[109]. But here we restricted homologous repeats (or conserved repeats) to those where both
species had repeats longer than expected by chance (Table S1).
Table S1. Genomic amino acid composition and minimum length of non-random
homopolymers.
Amino acids
a
Compositiona
p<0.05b
p<0.01 b p<0.001 b
Alanine (A)
0.035
6
7
7
Cysteine (C)
0.015
5
5
6
Aspartic acid (D)
0.053
7
7
8
Glutamic acid (E)
0.062
7
8
9
Phenylalanine (F)
0.049
7
7
8
Glycine (G)
0.044
6
7
8
Histidine (H)
0.019
5
6
6
Isoleucine (I)
0.083
8
9
10
Lysine (K)
0.079
8
8
9
Leucine (L)
0.09
8
9
10
Methionine (M)
0.016
5
5
6
Asparagine (N)
0.093
8
9
10
Proline (P)
0.042
6
7
8
Glutamine (Q)
0.045
7
7
8
Arginine (R)
0.03
6
6
7
Serine (S)
0.095
8
9
10
Threonine (T)
0.057
7
8
8
Valine (V)
0.047
7
7
8
Tryptophan (W)
0.008
4
5
5
Tyrosine (Y)
0.039
6
7
7
The fraction of the proteins in the complete predicted proteome consisting of the indicated amino acid.
b
The minimum length of a non-random amino acid homopolymer, for a given confidence level. Below these length
values, a given amino acid homopolymer could occur by chance as predicted by the overall amino acid composition
of the predicted proteome.
4
Figure S1. Number of occurrences of trinucleotide repeats (A) and homopolymer amino
acids (B) in Dictyostelium genomes. A. D. purpureum genome (circles) contains fewer and shorter
trinucleotide repeats than D. discoideum (triangles). Coding (solid circles and triangles) sequences has
more repeats than non-coding (open circles and triangles) sequences in both species. B. D. purpureum
proteome (circles) contains fewer and shorter homopolymer amino acids than D. discoideum (triangles).
Not shown are 1 D. purpureum and 2 D. discoideum repeats above 100 amino acids.
5
Figure S2. Codon usage within amino acid repeats and outside the repeats.
6
Figure S3. Codon diversity of homopolymer amino acid repeats. Codon diversity was
calculated as the probability that two random codons in a perfect amino acid repeat match each other:
d

k
N
(1  p 2 ) where N is the number of codons, i indexes the different codon types, and pi. is the
i
N 1
i
proportion of the amino acids in that sequence that are the ith codon. Codons of homopolymer amino acids
have higher diversity in D. purpureum than in D. discoideum (Mann-Whitney U test, p < 0.0001). Of the
box-and-whisker diagram, boxes show quartiles, whiskers show the most extreme data point which is no
more than 1.5 times the interquartile range from the box, and circles show outliers.
7
Figure S4. An example of pairwise sequence alignment of proteins with amino acid
homopolymers in both species. Protein sequences of DPU0062537 (dictyBase locus tag, upper
sequence, 363 residues) and DDB0233538 (lower sequence, 423 residues) from D. purpureum and D.
discoideum, respectively, were aligned by the program GAP4 and the BLOSUM62 matrix. The ‘.’ and ‘:’
above upper sequences mark the position of the consensus sequence; Between the upper and the lower
sequences, the ‘|’ mark matched residues; the ‘-’ and ‘+’ mark InDels; while mismatched residues are
showed by spaces.
8
Figure S5. Expression stages of genes with or without amino acid repeats. Panels A and C.
Genes with amino acid repeats have higher relative expression in the social or developmental stages in D.
purpureum (n = 1905, 3846, p < 0.0001, both Student’s t-test and Mann-Whitney U test) and D.
discoideum (n = 1600, 1439, p < 0.05, Student’s t-test; p < 0.0001, Mann-Whitney U test). The social
expression index measures a gene's relative expression in the social or developmental stage compared to
the vegetative stage (see Analysis of Social Genes below). Panels B and D. Genes with repeats had lower
vegetative-stage mRNA abundance, as measured by RNA-seq reads. Boxes show quartiles, whiskers
show the most extreme data point which is no more than 1.5 times the interquartile range from the box,
and circles show the outliers. Panels B and D. Genes with amino acid repeats have lower abundance of
vegetative ESTs than genes without amino acid repeats both in D. purpureum and D. discoideum
(Students t-test, both test p < 0.0001). Error bars show standard errors of the means.
9
Phylogeny
Orthologs were grouped by single linkage clustering of protein sequences on mutual-best
BLASTP hits from a colletion of pairwise genome comparisions: human [100] versus each of
(Oryzias latipes [100]; Gallus gallus, [100]; Branchiostoma floridae, JGI version 2 [13];
Nematostella vectensis, JGI version 1 [13]; Neurospora crassa, Broad release 7 [102];
Arabidopsis thaliana, TAIR8 [103]; Chlamydomonas reinhardtii, JGI version 4 [13];
Dictyostelium discoideum [14], plus D. discoideum vs each of (D. purpureum, Entamoeba
histolytica [22]). There were 389 clusters that had exactly one gene from each genome. For
each of these clusters, the protein sequences were aligned by ClustalW, and the alignments were
trimmed with default settings in Gblocks, leaving a mean of 216 filtered alignment columns per
ortholog group, and 83888 aligned columns in total, with no gaps or missing data. The
concatenated alignment was analyzed with mrbayes 3.1.2 using the WAG model, I+Gamma for
100,000 generations, with the first 50% of sampled trees discarded. The resulting consensus tree
was rooted at the midpoint of the branch connecting the green plants to the rest of the tree.
Figure S6. Synteny conservation between the D. purpureum and D. discoideum genomes
We identified blocks of approximately conserved gene order (supplemental Table S2) by clustering
together in the same block all pairs of genes that are within a threshold distance (w) of one another, and
have their orthologs in the other genome also within a distance (w), where w is the number of intervening
genes that have an ortholog in the other genome. The plot shows the rate of growth of these blocks of
conserved gene order as a function of increasing w for for D. purpureum versus D. discoideum to that for
permutation controls in which the gene orders were scrambled in both genomes. We found that up to w
10
values of approximately 15 intervening genes, clusters grow significantly faster than in the random
genome order expectation, which provides a conservative threshold for identifying blocks of
approximately conserved gene order. With this estimate 79% of orthologous gene pairs participate in a
block of approximately conserved gene order, compared to 5.8 +- 0.4% in controls, with a false positive
rate, on a gene-by-gene basis of ~7%.
Table S2. Syntenic blocks of genes (Separate Table).
The genes contained in the blocks of approximately conserved gene order are listed in the order
they are found in the D. discoideum genome.
Non-coding RNAs
Spliceosomal RNAs
The spliceosomal RNAs (rnUs) identified in D. discoideum, U1, U2, U4, U5, and U6, are each
characterized by both specific RNA-binding motifs and the ability to fold into specific secondary
structures [30, 31]. An initial BLAST search of these sequences against the D. purpureum
genome generated a collection of very short (~12 bp), exact matches. Each match was aligned
against its D. discoideum query sequence, and then extended in both directions to match the
length of the query sequence. Extended matches that overlapped in the D. purpureum genome
were merged. This generated a group of hits for each D. discoideum rnU. Each group was
aligned with the corresponding D. discoideum rnU, and the best-aligned sequences were selected
as putative homologs. These best hits all possess high sequence identity in the RNA-binding
regions of the rnU. Sequences with low conservation are mostly involved in self-binding, and
the differences between species are compensatory, in that similar structures can be formed.
When considering the large divergence between the two Dictyostelids, it is not surprising that
while secondary structures are conserved, the constituent bases are not.
tRNAs
11
We searched for tRNA genes and found at least one gene representing each amino acid (Table
S3b) [110]. Genes corresponding to the rare alanine tRNA with a GCG anti-codon were absent in
the intial assembly of the D. discoideum and presumed to be the unassembled portion of the
genome [1]. The presence of one such tRNA gene in the D. purpureum genome would support
the notion that these tRNA genes were not lost from the Dictystelids (Table S3b).
Table S3a. Non-coding RNA genes.
ncRNA
D. discoideum
In other Eukaryotes
Spliceosomal RNAs
D2/D9
snoRNAs
Antisense RNA
RNase RNA
tRNA
Found only in D. discoideum
Classes I & II
D1/Dd8
dutA
msRNA
D. purpureum
U1, U2, U4, U5, U6
First dictyostelid ncRNA
Box C/D, Box H/ACA
psvA
tRNA, rRNA processing
418 genes, all anticodons
U1, U2, U4, U5, U6
possible psvA
353 genes, all anticodons
Class I & II
yes
yes
yes
yes
-
Table S3b. tRNA genes in D. purpureum
Amino acid
Anti-codon
Ala
Ala
Ala
Arg
Arg
Arg
Arg
Asn
Asp
Cys
Gln
Gln
Glu
Glu
AGC
CGC
TGC
ACG
CCT
TCG
TCT
GTT
GTC
GCA
CTG
TTG
CTC
TTC
Number of
genes
17
1
4
7
1
1
9
17
21
6
1
12
2
20
Amino acid
Anti-codon
Gly
Gly
His
Ile
Ile
Leu
Leu
Leu
Leu
Leu
Lys
Lys
Met
Phe
GCC
TCC
GTG
AAT
TAT
AAG
CAA
CAG
TAA
TAG
CTT
TTT
CAT
GAA
Number of
genes
18
4
7
16
4
11
1
1
16
1
6
20
13
14
Amino acid
Anti-codon
Pro
Pro
Ser
Ser
Ser
Ser
Thr
Thr
Thr
Trp
Tyr
Val
Val
AGG
TGG
AGA
CGA
GCT
TGA
AGT
CGT
TGT
CCA
GTA
AAC
TAC
Number of
genes
1
15
5
1
6
13
15
1
5
7
12
17
4
The DUSE. A number of ncRNAs have a “Dictyostelium upstream sequence element”
(DUSE), an eight-nucleotide motif ([AT]CCCA[AT]AA) that sits ~63 base pairs upstream [111].
While the D. purpureum spliceosomal RNAs were identified using only the D. discoideum
spliceosomal RNA sequences, they also had a DUSE sitting ~63bp upstream.
12
To identify any potential ncRNAs downstream of the DUSE both genomes were first
masked for protein coding regions for D. pururpeum [112] and for D. discoideum [113]. Then
each genome was masked for low-complexity sequence via the dustmasker program in the NCBI
toolkit [22].
From these masked genomes, every instance of a relaxed DUSE motif
(/([ATCG]CCC(?(?<=[AC]CCC)A[^A]AA|A[ATCG]AA))/ as a Perl regular expression) was
identified, and each was associated with its Downstream Region (DSR), which consists of the
100 bp that sits 50 bp downstream of the DUSE. In D. discoideum, there are 7,409 DUSEs,
whose DSRs represent 2.1% of the entire genome and 3.1% of the unmasked bases in the
genome. In D. purpureum, there are 11,234 DUSEs, whose DSRs represent 3.4% of the entire
genome and 3.4% of the unmasked bases in the genome.
Next each 8-mer was counted in both the entire masked genome and the DSR, for each
dictyostelid, and combined to give an occurrence ratio (the number of times an 8-mer occurs in
the DSRs divided by the number of times an 8-mer occurs in unmasked genome) (Figure S7,
Table S4). Three 8-mers are found to have the three highest DSR occurrence ratios in both
Dictyostelids (>0.29 in each genome). The significance of this trio was assessed by performing
the same analysis for all 8-mers that occur in the genome approximately the same number of
times as the relaxed DUSE motif (between 4,500 and 14,500 times in each genome). For each of
these control 8-mers, DSRs were extracted from each masked genome, and downstream 8-mer
occurrence ratios were calculated as they were for the DUSE. Out of 879 control 8-mers, there
were none that had an 8-mer with occurrence ratios > 0.3 in both genomes, and one that had two
13
D. discoideum
A.
occurrences
in masked
DSR
occurrences
in masked
genome
D. purureum
occurrence
ratio
occurrences
in masked
DSR
occurrences
in masked
genome
occurrence
ratio
Upstream
Sequence
8-mer
DUSE
DUSE
CTTACAGC
CCTTACAG
28
46
0.61
27
61
0.44
29
47
0.62
29
99
0.29
DUSE
TTACAGCA
30
103
0.29
28
178
0.16
DUSE
TACAGCAA
32
102
0.31
28
250
0.11
DUSE
TTCCTTAC
19
117
0.16
30
150
0.2
DUSE
TCCTTACA
13
88
0.15
29
120
0.24
DUSE
CTAGCAGA
17
34
0.5
16
38
0.42
AAAAACTT
AAGCTAAG
18
62
0.29
13
68
0.19
AAGAATTA
TTCAGAGG
12
74
0.16
17
110
0.15
AAATCCAA
ATAGTTCC
13
80
0.16
38
207
0.18
AATCCAAA
ATAGTTCC
13
80
0.16
38
207
0.18
AATCCAAA
GTGGAATC
13
83
0.16
19
118
0.16
ATAATTAT
AAAAAATA
664
2418
0.27
610
3647
0.17
ATAATTAT
ATAAAAAA
621
2152
0.29
577
3489
0.17
ATAATTAT
TATTTTTT
590
2418
0.24
676
3647
0.19
ATAATTAT
TTTTTTAT
621
2152
0.29
599
3489
0.17
ATTATAAT
ATTATAAT
ATTATAAT
ATTATAAT
ATTATAAT
ATTATAAT
AAAAAATA
ATAAAAAA
TATTTTTT
TTTTTTAA
TTTTTTAT
TTTTTTCT
543
531
612
439
557
116
2418
2152
2418
2584
2152
507
0.22
0.25
0.25
0.17
0.26
0.23
710
666
832
725
781
171
3647
3489
3647
3639
3489
1085
0.19
0.19
0.23
0.2
0.22
0.16
B.
Figure S7. Occurrence of 8-mer sequences downstream of DUSE elements. A. In blue are the
all the DUSE-enriched 8-mers with occurrence ratios >0.2 in both genomes. Six of these seven 8-mers are
subsequences of the NSBR in the classes I and II ncRNAs. In red are all 8-mers (second column) enriched for by
14
some control DUSE (first column) with occurrence ratios >0.15 in both genomes. B. Each blue point represents an
8-mer that sits in the DSRs of the DUSE. Only those 8-mers that have occurrence ratios >0.1 in both genomes are
shown for the 879 Control DUSEs (red). The three 8-mers with the highest ratios, in the upper right-hand corner of
the plot, are CCTTACAG, CTTACAGC, and CTAGCAGA.
8-mers with occurrence ratios >0.2. Figure S7 shows that the 8-mers of the DUSE trio each have
higher occurrence ratios than any of the sequences enriched for by the control 8-mers.
Identification of D. purpureum class I and class II homologs. The most DUSEenriched 8-mer, CTTACAGC, starts in the second position of NSBR of the class I and class II
ncRNAs (Figure 4). To identify putative homologs in D. purpureum, each occurrence of this 8mer was identified in both D. purpureum and D. discoideum. Of the 46 occurrences of the 8-mer
in D. discoideum, 28 possess an upstream DUSE within 100 bp. For each of these 28, a 5'-stem
sequence was identified as the 5 bp that sit 6 bp upstream of the 8-mer. The closest sequence
that was both complementary to the 5'-stem and sat between 20 bp and 100 bp downstream of the
8-mer was identified as the 3'-stem. 26 of the 28 sequences had 5'/3' complementary sequences.
These 26 all corresponded to previously identified classes I and II ncRNAs in D. discoideum
(Figure S8). The same analysis was performed on D. purpureum, identifying 61 instances of
the 8-mer, 27 of which had an upstream DUSE. 26 of those also had 5'/3' complementary
sequences. These 26 sequences constitute the putative D. purpureum ncRNAs. Because they all
share the same 5'-stem sequence, they might be considered putative class I ncRNAs.
To assess the secondary structure of these putative ncRNAs, all 52 sequences, from both
dictyostelids, were aligned structurally using the locARNA [114] (Figure S8). This alignment
and structure was then passed to RNAlogo server [115]. This provided an image that was
adapted for Figure 4.
15
Dd_r49
Dd_r52
Dd_r21
Dd_r22
Dd_r23A
Dd_r23C
Dd_r24A
Dd_r24B
Dd_r25
Dd_r26
Dd_r28
Dd_r29
Dd_r30
Dd_r31
Dd_r32
Dd_r33
Dd_r41
Dd_r42
Dd_r44
Dd_r46
Dd_r47
Dd_r59
Dd_r60
Dd_r62
Dd_r35
Dd_r36
GUUUACCUUACAGCAAA-UCUUACAGUUCCUUCAUUCUAAGAAAACCUUCCGUCAACUGUCUUUUUUUUAAUUG-UUUGUUAUGGAU
GUUGACCUUACAGCAAA-UCCUGCAGUUCCUUCAUUCUAAGAAAACCUUUCGCCAACUGUCUUUUUUAUA-----------AUUAAU
GUUGACCUUACAGCAAACCCUAC-------AGU---CAUUUCAU--------------------AAGAAAAAC----UACCGUCAAC
GUUGACCUUACAGCAAAUCUAAC-------AUUUCCUUACAUUC--------------------AAAGAAAAC----CUUUGUCAAC
GUUGACCUUACAGCAAAUCUAAC-------AUUUCCUUACAUUC--------------------AAAGA-AAC----CUUCGUCAAC
GUUGACCUUACAGCAAAUCUAAC-------AUUUCCUUACAUUC--------------------AAAGA-AAC----CUUCGUCAAC
GUUGACCUUACAGCAAAUCUUAC-------AGUUCCUUCAUUCU--------------------AAGAAAACC----CUCCGUCAAC
GUUGACCUUACAGCAAAUCUUAC-------AGUUCCUUCAUUCU--------------------AAGAAAACC----CUCCGUCAAC
GUUGACCUUACAGCAAAUCUUAC-------AGUUCCUUCAUUCU--------------------AAGAAAACC-----UCCGUCAAC
GUUGACCUUACAGCAAAUCUUAC-------AGUUCCUUCAUUCU--------------------AAGAAAACC----UUCCGUCAAC
GUUGACCUUACAGCAAUCUAAUC-------ACAAAUUUUUACUUCAC-----------------AAAAAAAAAACCCCUUCGUCAAC
GUUGACCUUACAGCAAUUC--AU-------UCUCUACAUAAA----------------------AAGAAAACC----CCCUGUCAAC
GUUGACCUUACAGCAAUUCUCAC-------AUUUCCUUACAUUC--------------------AAAGAAAAC----CUUCGUCAAC
GUUGGCCUUACAGCAAAUUCUCA-------CAAAUUUUUACUGAUUA-----------------AAAAAAACC----CCUUGUCAAC
GUUGACCUUACAGCAAAUCUUAC-------AAU---UUCAUCCU--------------------AAGAAAAAA----UACAGUCAAC
GUUGACCUUACAGCAAAUCCUCU-------CAAAUUUUUACUGAUU------------------AAAAAAACC----CCUCGUCAAC
GUUGACCUUACAGCAAAUCUUAA-------AGCUACUUCAUUCU--------------------AAGAAAAAC----UCCUGUCAAC
GUUGACCUUACAGCAAAUAUCAC-------AGAUUAAAAACCCU-------------------------------------GUCAAC
GUUGGCCUUACAGCAAACCU-UU-------GAAGAUUACCCCUU-------------------------------------GUCAAC
GUUGACCUUACAGCAAAUUAUCA-------UUCUACAGGAAGA-----------------------AAACCA-------UUGUCAAC
GCUGACCUUACAGCAAUUCUAUC-------ACU--CUACAUUCC--------------------AAAGAAAUC----CUUCGUCAGC
GUUGACCUUACAGCAAUCUUAAC-------AAUUUUAUCACAUU--------------------AUAAAAAAA-----AACCUCAGU
GUUGACCUUACAGCAAUCUUAAC-------AAAAUUUUUUCUGAAUA-----------------AAAAAA--C----CUAAGUCAAC
GUUGACCUUACAGCAAAUCU-UG-------CAGAA--AACCUUA-------------------------------------GUCAAC
GCUCGCCUUACAGCAAUUACUCU-------G-AUUUUUCUCCAA--------------------AAAAAAAAC----CUUCGCGAGU
GCUCGCCUUACAGCAAUUACUCU-------GAAUUUUUCUCCAA--------------------AAAAAAACC----CUUCGCGAGU
Dp_1
Dp_10
Dp_11
Dp_12
Dp_14
Dp_15
Dp_17
Dp_18
Dp_19
Dp_2
Dp_20
Dp_22
Dp_23
Dp_24
Dp_25
Dp_4
Dp_7
Dp_8
Dp_9
Dp_13
Dp_16
Dp_21
Dp_26
Dp_3
Dp_5
Dp_6
GAAUUCCUUACAGCAAUGA--CU-------CAUCUGAAACCCUU-------------------------------------GGAUUC
GAAUUCCUUACAGCAAU--AUAA-------C--AUUCAAAAUUUAAC-----------------UCUGAAAU------CUUGAAUUC
GAAUUCCUUACAGCAAUUAAACU-------C--AUUCAAAAUUUAAC-----------------UCUGAAAU------CUCGAAUUC
GAAUUCCUUACAGCAAUUUAAUC-------AUAAUCAAAUUACUCAC-----------------UUGAAAAAAA---CCUUGGAUUC
GAAUUCCUUACAGCAAUUUAAUA-------AAAAUCAAAUUACACAC-----------------UUG---AAAA---CCUUGGAUUC
GAAUUCCUUACAGCUAUUUAUAU-------CAAAUCAAAUUUCUCAC-----------------UUGA--AAAC---CUUUGGAUUC
GAAUUCCUUACAGCAAUUUAGCU-------C--AUUCAAAAUUUAAC-----------------UCUGAAAU------CUCGAAUUC
GAAUUCCUUACAGCAAU--AACU-------C--AUUCAAAAUUUAAC-----------------ACUGAAAU------CUUGAAUUC
GAAUUCCUUACAGCAAUAAACUU-------GACUCUGAAAUCUU-------------------------------------AAAUUC
GAAUUCCUUACAGCAAUUA-CAU-------UAUUGAAGAAACCU-------------------------------------GAAUUC
GAAUUCCUUACAGCAAUAUAACU-------C--AUUCAAAAUUUAAC-----------------UCUGAAAU------CUCGAAUUC
GAAUUCCUUACAGCAUUUUAUCU-------CUCUUUGAAUUCGGUUA-----------------GUAUCGAAAG-AUAUUGGGGUUC
GAAUUCCUUACAGCAAUUGAUAC-------AUUUUCCCUCCC----------------------AAAGAAAAA----AACCGAAUUC
GAAUUCCUUACAGCAACACAUAC-------AUAAUCUAAAAUCAUAU-----------------UUUUAAGAAA---CUUUGGAUUC
GAAUUCCUUACAGCAAUCAUUAA-------UGAAUGUUCAUCUU---------------------GAGAGACC----CACGUGGUUU
GAAUUCCUUACAGCAAUUG--AC-------AUUUUCCCUCCC----------------------AUAGAAAAA----AUCCGAAUUC
GAAUUCCUUACAGCAAUUG--AC-------AUUUUCCCUCCC----------------------AAAGAAAAA----AACUGAAUUC
GAAUUCCUUACAGCAAUUA--AA-------UCAAUUCACUCA----------------------UUUGAAAAA----CCUUGGAUUC
GAAUUCCUUACAGCAAUGAUUUA-------AACAA-UUAGUUA-----------------------UGAAAA-------UCGGGUUC
GAAUUCCUUACAGCAAUGAAAUGAUG----AUCUGGAGAGACCCACUCAUUAGAGAACCAUGGGUCUUUCCGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUGAAAAGAUG----AUCUGGAGAGACCCACUCAUUAGAGAACAAUGGGUCUUUCCGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUGAAAUGAUG----AUCUGGAGAGACCCACUCAUUAGAGAACCAUGGGUCUUUCCGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUGAAAUGAUG----AUCUGGAGAGACCCACUCAUUAGAGAAACAUGGGUCUUUCCGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUCAAAAGUUU----AUCUUGAGAGGCCCACU---------------GGUCUUUCUGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUGAAAUGAUG----AUCUGGAGAGGCCCACUCAUUAGAGAACCAUGGGUCUUUCCGGGAAAAAUUGGAUUC
GAAUUCCUUACAGCAAUGAAAUGAUG----AUCUGGAGAGGCCCACUCAUUAGAGAACCAUGGGUCUUUCCGGGAAAAAUUGGAUUC
(((((.............((((.-------..(((((((((......-----------------))))))))).....)))))))))
Figure S8. Sequences of putative novel non-coding RNAs in D. purpureum and D.
discoideum. All 52 identified classes I and II ncRNAs are structurally aligned.
16
Protein-coding gene product prediction
Protein Ortholog Discovery
A list of orthologous genes between D. purpureum and D. discoideum was created using three
sources (in order of confidence): manual curation (as of February 2009), and the Inparanoid
algorithm [116], and Best bidirectional blast algorithm. Briefly, both algorithms find reciprocal
best match between amino acid sequences using BLASTP. All of the D. discoideum gene models
from the May 2009 genome build of dictyBase were blasted against all the D. purpureum gene
models. The Inparanoid algorithm has the advantage of finding one-to-many or many-to-many
relationships, by using the reciprocal best matches as seeds to cluster additional orthologs. A
minimum cutoff for similarity of 50 bits and 50% overlap was used to avoid inclusion of
insignificant hits.
The predictions from the Inparanoid algorithm were validated using the manually curated
list. Of the 5,826 one-to-one ortholog pairs identified, 205 had been manually curated. Of those
205 Inparanoid predictions, 202 agreed with the manual curation.
Table S4. (Summary of Additional Data File 2)
Source
Number of orthologs
Manual Curation (February
2009)
Inparanoid
257
Reciprocal Best Match
1,536
Total Orthologs
7,619
5,826
The complete list of orthologs can be found in the Supplemental Table S4 Excel file.
There are 2,759 additional D. pupureum genes and 2,990 genes in D. discoideum that are
paralogous, but where one-to-one orthologous relationships could not be determined
(Supplemental Table S5, as separate Excel Table). These families probably represent small gene
groups that underwent duplication and divergence soon after the split of the last common
ancestor of D. pupureum and D. discoideum. There are also 2,001 genes in D. pupureum genes
and 3,531 genes in D. discoideum that failed to match any gene in the other genome with a bit
score higher than 50.
17
Total genes in D. discoideum
Genes mapped to D. purpureum
orthologs
Figure S9. Proportion of orthologous genes between D. purpureum and D. discoideum in
major gene families. Histogram of the number of D. discoideum genes that have clear othologs in D.
purpureum for the 127 gene families listed in Legend below. Gene families (in blue) are listed with their
18
annotations, the number of members in the D. discoideum reference genome and the number of those
members that have clear orthologs in D. purpureum. Only automated gene product annotations were used,
so the numbers of genes in each family will change as manual annotation refines the gene product
predictions.
Gene
Family
abc
Total
in
D.d.
67
Orthologs in
D.p.
41
Gene
Family
irl
Total
in
D.d.
8
5
1
jcd
kif
9
13
9
tgr
16
10
lim
7
6
lsm
8
8
lvs
7
BEACH domain-containing protein
7
13
acetylornithine deacetylase
actin related protein 2,
polyphosphate kinase component
ADP-ribosylation factor-related,
ARF-related
Annotation
IRE family protein kinase
transcription factor jumonji, jmjC
domain-containing protein
kinesin family member 9
IPT/TIG domain-containing protein,
immunoglobulin E-set domaincontaining protein (Tiger protein)
LIM-type zinc finger-containing
protein
LSM (like-Sm) protein, U6 small
nuclear RNP-associated protein
abp
act
7
39
alg
9
ana
10
arg
7
arp
8
arr
4
man
8
6
asl
29
putative acetyl-CoA synthetase
2
mcf
26
atg
13
13
mcm
8
atp
11
autophagy protein 4
ATPase subunit 1, ATP synthase
F1 alpha
alpha-mannosidase
mitochondrial substrate carrier
family protein
MCM family protein, putative DNA
replication licensing factor
8
med
27
bzp
cap
17
8
putative basic-leucine zipper
(bZIP) transcription factor
cAMP-binding protein
9
6
mrp
myb
25
27
cbp
17
8
myo
12
cct
7
7
nad
11
cdc
10
9
nag
7
cdk
8
6
ndu
10
clc
7
7
nol
9
cnr
12
10
nup
10
cof
8
1
omt
11
cog
8
cofilin-2
oligomeric Golgi complex
component
8
osb
12
com
18
NAD-dependent aldehyde
dehydrogenase
14
pak
9
coq
10
ubiE/COQ5 methyltransferase
family protein
8
pex
14
cpn
7
phospholipid-binding protein,
copine A
3
pig
16
Annotation
ABC transporter G family protein
alpha actinin, actin bundling
protein
actin
glycosyltransferase, beta-1,4mannosyltransferase
anaphase promoting complex
subunit 11
calcium-binding protein
chaperonin containing TCP1 eta
subunit
cell division cycle protein 48,
CDC48 family AAA ATPase
p34-cdc2 protein, protein
serine/threonine kinase, cyclindependent kinase, CMGC group
clathrin light chain
cleft lip and palate
transmembrane 1 family protein,
putative cell number regulator
19
Orthologs in
D.p.
1
8
9
3
6
8
22
8
putative mediator complex subunit 8
S60 ribosomal protein L11,
ribosomal protein L11,
mitochondrial
myb transcription factor
class VII unconventional myosin,
myosin VII
24
NADH dehydrogenase subunit 4
beta-N-acetylhexosaminidase,
glycoside hydrolase family 20
protein, beta-hexosaminidase
ubiquinone oxidoreductase, NADH
dehydrogenase ubiquinone
flavoprotein 1
pseudouridine synthase family
protein, DKCLD domain-co protein,
PUA domain, H/ACA RNP complex
subunit 4
1
nucleoporin 107
O-methyltransferase family 2
protein
oxysterol binding family protein,
member 1
p21-activated protein kinase,
protein serine/threonine kinase,
STE20 family protein kinase, PAKA
subfamily protein kinase
WD40 repeat-containing protein,
peroxisomal biogenesis factor 7,
peroxin 7, peroxisome targeting
signal type 2 receptor
GlcNAc transferase,
phosphatidylinositol glycan, class A,
phosphatidylinositol Nacetylglucosaminyltransferase
subunit A, glycosyltrasferase
11
20
12
5
10
9
10
5
9
8
13
16
cpr
9
cysteine proteinase 5 precursor
7
pik
8
crl
7
7
pks
44
csn
9
cAMP receptor-like protein, Gprotein-coupled receptor (GPCR)
family protein
putative casein kinase II beta
chain (CK2)
8
plb
7
cup
cyc
9
8
1
8
pol
pon
cyp
60
25
ddx
19
dg1
22
dhk
14
dhx
did
8
7
dsc
7
dst
dyn
ecm
8
7
11
eif
30
exo
10
fam
9
fnk
8
for
10
fsc
9
fsl
18
fut
11
gac
32
gcv
7
gdt
10
gef
25
gnt
15
calcium up-regulated protein,
ricin B lectin domain
cyclin, G2/M-specific cyclinB
cyclophilin E, cyclophilin-type
peptidylprolyl cis-trans isomerase
(PPIase)
putative RNA helicase,
DEAD/DEAH box helicase
RING zinc finger-containing
protein, Kelch repeat-containing
protein
Atypical group, HisK family
protein kinase
DEAD/DEAH box helicase,
putative RNA splicing factor
discoidin II
signal transducer and activator of
transcription (STAT) family
protein
dynactin 150 kDa subunit
extracellular matrix protein ST310
eukaryotic translation initiation
factor 5A
5'3'-exonuclease N- and Idomain-containing protein,
putative exodeoxyribonuclease I
DUF59 family protein, FAM96
family protein
FNIP repeat-containing protein,
protein kinase, STE group
actin binding protein, formin
homology domain-containing
protein
G-protein-coupled receptor
(GPCR) family protein, frizzled
and smoothened-like sans CRD
G-protein-coupled receptor
(GPCR) family protein, frizzled
and smoothened-like protein
glycosyltransferase, alpha-3/4fucosyltransferase
RhoGAP domain-containing
protein
glycine dehydrogenase
(decarboxylating), glycine
cleavage system P-protein
GDT family protein kinase
Ras guanine nucleotide
exchange factor
GlcNAc transferase, UDPGlcNAc:hydroxyproline
phosphatidylinositol-4,5diphosphate 3-kinase, PI3kinase
short-chain
dehydrogenase/reductase (SDR)
family protein, 3-oxoacyl-[acylcarrier protein] reductase
8
6
6
9
15
phospholipase B
mitochondrial DNA polymerase A,
5'-3' exonuclease domaincontaining protein, 3'-5'
exonuclease domain
actin binding protein, ponticulin
prp
13
Propionate catabolic protein PrpD.
12
18
psi
20
PA14 domain-containing protein
10
19
psm
42
proteasome subunit alpha type 7,
20S proteasome subunit alpha-7
39
13
psp
7
6
NA
pur
rab
8
60
2
rac
21
7
7
4
rad
ras
rnu
7
11
18
29
roc
8
10
rpb
12
9
rpc
9
3
rpl
48
S60 ribosomal protein L36
42
10
rps
32
40S ribosomal protein S4
30
5
rsm
13
small GTPase
9
sam
7
5
sec
12
29
sf3
8
6
sig
11
1
sno
19
25
snr
11
7
sod
7
20
prespore protein
adenylosuccinate synthetase
Rab GTPase
Rho GTPase, RhoBTB family
protein
DNA repair protein Rad4 family
protein
Ras GTPase
snRNA, small nuclear RNA
WD40 repeat-containing protein,
protein kinase, tyrosine kinase-like
protein, ROCO family protein kinase
RNA polymerase II largest subunit,
RNA polymerase II core subunit
putative RNA polymerase III
subunit, putative RNA polymerase I
subunit
SAM domain-containing protein,
SAMK family protein kinase
ankyrin repeat-containing protein,
pleckstrin homology (PH) domaincontaining protein, Arf guanylnucleotide exchange factor
C2H2-type zinc finger-containing
protein, splicing factor 3A subunit 3
unknown
C/D-box small nucleolar RNA, C/D
box snoRNA
U1 small nuclear ribonucleoprotein
70 kDa protein
superoxide dismutase
8
2
3
8
31
11
6
6
NA
7
10
9
5
NA
11
8
10
NA
10
4
polypeptide alpha-Nacetylglucosaminetransferase
gp1
7
cell surface glycoprotein gp138
NA
srp
11
gpa
12
G-protein subunit alpha 7
10
syn
11
gpt
10
3
taf
9
grl
16
10
tbc
7
gta
23
10
tme
16
gtf
14
13
tra
8
gxc
37
37
ubq
15
hbx
14
11
utp
9
hel
7
7
vat
8
hem
8
8
vps
hsp
27
12
wdr
int
8
putative glycophosphotransferase
G-protein-coupled receptor
(GPCR) family 3 protein 14
putative GATA-binding
transcription factor
transcription initiation factor IIA
gamma chain
pleckstrin homology (PH)
domain-containing protein,
RhoGEF domain-containing
protein, armadillo repeatcontaining protein
putative homeobox transcription
factor, homeodomain (HOX)
putative RNA helicase,
DEAD/DEAH box helicase
putative uroporphyrinogen III
synthase
heat shock protein, heat shock
cognate protein Hsc70-2
type A von Willebrand factor
(VWFA) domain-containing
protein, initiation factor eIF-4
gamma middle domaincontaining protein, integrator
complex subunit 6
signal recognition particle 54 kDa
subunit
putative t-SNARE family protein,
putative syntaxin 6
putative protein serine/threonine
kinase, bromodomain-containing
protein, transcription initiation factor
TFIID subunit, TFIID subunit,
protein kinase, Atypical group,
TAF1 family protein kinase, HAF
group protein
RabGAP/TBC domain-containing
protein, TBCK family protein kinase
transmembrane protein, DUF786
family protein
heat shock protein Hsp90 family
protein
ubiquitin/ribosomal protein S27a
fusion protein
U3 snoRNP protein, U3 small
nucleolar ribonucleoprotein
8
8
9
7
14
6
4
9
38
vacuolar H+-ATPase E subunit
vacuolar protein sorting-associated
protein 26
8
36
21
WD40 repeat-containing protein
21
8
Predicted proteins present in D. purpureum and absent in D. discoideum
There are 2,001 of the 12,410 predicted D. purpureum genes that have no obvious counterpart in
D. discoideum (Table S5). Many of these are likely to be erroneous predictions or gene
fragments that will be clarified upon more extensive annotation over time. Even given this
uncertainty, there are a number of well annotated proteins in D. purpureum that appear to be
absent in D. discoideum, although some of these may point to gaps in the D. discoideum genome.
Also, as the manual annotation of both genomes progresses, the presence of any of these
predicted gene products may be revealed. Among the annotated genes only 8 characterized D.
discoideum genes did not have identifiable homologs in the current D. purpureum assembly.
Two of these 8, ponA and ponB, are related to each other and reside on different chromosomes in
D. discoideum, so they are likely to be a true difference in gene content between the two species.
If all of the other 6 missing genes represent true gaps in the D. purpureum sequence, it would
suggest that we are missing, roughly, <0.1% of the D. purpureum genes in our current assembly.
21
* 158581 (D. purpureum protein I.D) / DPU_G0068098 (dictyBase Gene I.D): D. purpureum
has 2 neks, and D. discoideum has 3. D. discoideum has nek2, nek3,and nek4, and D. purpureum
has only nek3 and the nek6-like.
* 160185 / DPU_G0073346: TruB homolog; IPR002501 and IPR014780 tRNA pseudouridine
synthase B, N-terminal, bacterial-type; while D. discoideum seems to have tRNA pseudouridine
synthase D, there is no tRNA pseudouridine synthase B; TruB1 homolog animals.
* 75000 / DPU_G0055928: Chitin binding protein.
* 91849 / DPU_G0075114, 96643 / DPU_G0058838, 151171 / DPU_G0075100, 149996 /
DPU_G0071494: several copies of chitinase II (the related family PTHR11177 is present, but not
IPR011583 (SM00636) in Entamoeba histolytica as well.
* 96521 / DPU_G0054712, 91204 / DPU_G0054716, 147640 / DPU_G0054714: Sulfatasemodifying factor; this domain is absent from D. discoideum and S. cerevisiae. From InterPro
entry (IPR005532): SUMF1 is a paralogue of oxoalanine-generating enzyme, also called
C(alpha)-formylglycine generating enzyme (FGE). SUMF1 converts newly synthesized inactive
sulfatases to their active form by modifying an active site cysteine residue to oxoalanine.
Sulfatases are essential for the degradation of sulphate esters, whose catalytic activity is
dependent upon an oxoalanine residue.
* 148893 / DPU_G0065326: CORD and CS domain protein (cysteine and histidine-rich domain
(chord)-containing protein), similar to Integrin beta-1-binding protein 2 (Q9UKP3).
* 11178 / DPU_G0066964, 11201 / DPU_G0069136: keratin associated protein; domain
PD010562 - neither protein nor domain is in D. discoideum.
* 78213 / DPU_G0075718: barnase inhibitor: Extracellular ribonuclease of Bacillus
amyloliquefaciens. The gene is not present in eukaryotes, so this gene may be in the D.
purpureum genome as the result of a horizontal gene transfer.
* 91798 / DPU_G0074254: phosphocarrier protein HPr - bacterial ptsH; however this is a
complex, and the other subunits, ptsI or crr, do not seem to be present. The gene is not present in
eukaryotes, so this gene may be in the D. purpureum genome as the result of a horizontal gene
transfer.
* 152726 / DPU_G0053860: cation transport regulator ChaB; however, chaA is absent, chaB
function is unknown, and predicted to be a regulator. chaC is present in D. discoideum and in
most eukaryotes (associated with the putative ChaA Ca2+/H+ cation transport protein in
Escherichia coli; function unknown; Dicty has another family of Ca2+/H+ transporters). The
chaB gene is not present in eukaryotes, so this gene may be in the D. purpureum genome as the
result of a horizontal gene transfer.
22
* 156106 / DPU_G0061782: very conserved to fungal and bacterial proteins; IPR005247 YbhB
and YbcL; bacterial PBP family phospholipid-binding protein / PEBP family protein; there are
no blast hits to any other amoeba.
* 157748 / DPU_G0065844: conserved in tetrahymena and branchiostoma, a chordate, but no
conserved domains.
* 82874 / DPU_G0063878 minD, 84186 / DPU_G0067936 minE: involved in septum formation
in bacterial species (possibly involved in mitochondrial replication).
Polyketide Synthases
Pfam HMMs were used to identify the keto-acyl synthase (ketoacyl-synt and Ketoacylsynt_C) and the acyl-transferase (Acyl_transf_1) domains from the 40 D. discoideum and 52 D.
purpureum PKS sequences [117]. The sequences of these domains were aligned using the
Muscle program [118] and the alignment manually edited. Phylogenetic analysis was carried out
by the UPGMA and neighborjoining methods using the MEGA4 package [119]. The UPGMA
and neighbour-joining trees were obtained using the MEGA4 package with distances calculated
using the JTT matrix. Trees were similar and were independent of the method used. All file
manipulations and data processing were carried out using custom written PERL scripts. All the
files can be obtained from the MRC website [120].
Table S6. The Polyketide Synthases of D. purpureum and D. discoideum. The identifying
numbers of the genes used in Figure 5A and the corresponding gene predictions at dictyBase at
[14], as well as the number of amino acids, is given. Only the genes used in the figure are
included. Predictions as well as the number of amino acids are given.
D.d. Gene
AA
1
2
3
4
5
6
7
8
2603
2604
3010
2499
2499
3097
3078
2531
D. discoideum
dictyBase
Gene I.D.
DDB_G0275069
DDB_G0275077
DDB_G0270572
DDB_G0283931
DDB_G0284001
DDB_G0293912
DDB_G0293902
DDB_G0288457
D.p.
Gene
AA
1
2
3
4
5
6
7
8
2736
2516
3003
2500
2557
2497
1925
2482
23
D.purpureum
Protein
I.D. Number
159351
147207
56948
148809
148808
28523
98568
76035
D.purpureum
dictyBase
Gene I.D.
DPU_G0070338
DPU_G0074440
DPU_G0059924
DPU_G0064650
DPU_G0064648
DPU_G0064654
DPU_G0058036
DPU_G0065412
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
stlA
stlB
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
2485
2542
2552
2931
2931
2924
2514
2514
2513
2512
2837
2380
2471
2551
3174
2999
2998
2779
2778
2658
3075
3106
3101
2623
3078
3127
3108
3133
2690
2684
3147
2968
DDB_G0271662
DDB_G0291684
DDB_G0291614
DDB_G0295659
DDB_G0271530
DDB_G0271524
DDB_G0295667
DDB_G0271618
DDB_G0271614
DDB_G0271520
DDB_G0271000
DDB_G0287095
DDB_G0287119
DDB_G0272981
DDB_G0273007
DDB_G0281475
DDB_G0272859
DDB_G0282029
DDB_G0282027
DDB_G0292544
DDB_G0290701
DDB_G0290699
DDB_G0290709
DDB_G0290703
DDB_G0290737
DDB_G0290729
DDB_G0290943
DDB_G0290937
DDB_G0290469
DDB_G0290467
DDB_G0269364
DDB_G0290853
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
2504
2373
2481
2973
2917
2971
2966
2756
2336
2499
2737
2735
2882
2722
2646
2919
2560
2361
2525
2936
2939
2930
2953
2974
2961
2956
2535
2949
2952
2493
2392
2527
2524
2361
2532
2530
2523
2420
2531
2523
2535
2536
2535
2534
24
148800
38743
54214
153779
88429
147609
156533
149063
149064
149067
149068
149069
14379
14334
147748
36677
155872
96815
48793
56925
157297
157296
153367
94806
148728
158551
153368
153366
158552
89013
86974
148565
152464
84141
55899
158676
87448
88993
146538
153476
35211
154925
28418
75833
DPU_G0064628
DPU_G0061162
DPU_G0072748
DPU_G0056128
DPU_G0055732
DPU_G0054664
DPU_G0062936
DPU_G0066546
DPU_G0066548
DPU_G0066554
DPU_G0066556
DPU_G0066558
DPU_G0060068
DPU_G0075164
DPU_G0055892
DPU_G0057886
DPU_G0061120
DPU_G0062778
DPU_G0056916
DPU_G0059880
DPU_G0064756
DPU_G0064754
DPU_G0055200
DPU_G0063950
DPU_G0068050
DPU_G0055202
DPU_G0068052
DPU_G0059302
DPU_G0071454
DPU_G0062782
DPU_G0053260
DPU_G0067840
DPU_G0055516
DPU_G0068352
DPU_G0075108
DPU_G0059218
DPU_G0051208
DPU_G0055518
DPU_G0055514
DPU_G0058958
DPU_G0063914
DPU_G0063918
ATP-binding Cassettee (ABC) Transporters
The ABC super-family is one of the largest in both bacteria and eukaryotes.
ABC proteins all have a conserved 200-250 amino acid long domain, the ATP-binding
cassette, that gives them their family name. In addition many have transmembrane
domains that function in transport of a variety of compounds across membranes. Seven
different eukaryotic families have been defined on the basis of sequence homology,
domain topology and function. The ABC super-family in D. discoideum was analyzed
early during genome assembly and annotation [43]. Members of the D. purpureum
ABC super-family were manually curated and compared in detail to the D. discoideum
members. Both genomes carry similar numbers of ABC genes overall, but gene
“gains” and “losses” can be observed within specific families (Table 1). However,
only 58 genes can be considered clear orthologs, the others being paralogs. Most of the
variation in gene number is observed in groups of closely related genes belonging to
the largest families. These genes probably play partially redundant roles and their
number can drift randomly. On the other hand, unique genes tends to be conserved and
to present only one ortholog. Orthologous ABCs in these Dictyostelids show 66%
amino acid identity, on average, similar to other genes.
Table S7: Genes in the ABC Superfamily.
Gene families
ABCA family
Full
Half
ABCB family
Full
Half
D. discoideum
D. purpureum
Differences*
7 genes
5 genes
6 genes
3 genes
+1
+2
2 genes
9 genes
3 genes
9 genes
-1
0
ABCC family
ABCD family
Full
Half
ABCE family
ABCF family
ABCG family
Full
half
Other**
13 genes
8 genes
+5
None
3 genes
1 gene
4 genes
None
3-4 genes
1 gene
4 genes
0
0
0
0
14 genes
9 genes
6 genes
17 genes
14 genes
6 genes
-3
-5
0
Total
73 genes
75 genes
-2
* The difference in gene number is D. discoideum, minus D. purpureum.
** “Other” ABC genes includes the ArsA homologues but not the SMC group.
25
Table S8. ABC transporter genes of D. purpureum and D. discoideum.
Gene
abcB1
abcB2
abcB3
abcB4
abcB5
dictyBase
Gene I.D.
DPU_G0075094
DPU_G0061498
DPU_G0067284
DPU_G0052882
DPU_G0069080
DPU_G0063470
DPU_G0065562
DPU_G0075092
DPU_G0075090
DPU_G0062718
DPU_G0067740
DPU_G0057272
DPU_G0061998
DPU_G0054084
abcB6
abcB7
abcB8
DPU_G0052826
DPU_G0062650
DPU_G0057426
tagA
tagB
tagC
DPU_G0071860
DPU_G0059398
DPU_G0059394
tagD
abcC2
abcC3
abcC5
abcC8
abcC9
DPU_G0071556
DPU_G0054216
DPU_G0065712
DPU_G0075734
DPU_G0068514
abcA1
abcA2
abcA3
abcA4
abcA5
abcA6
abcA8
abcA9
abcC10
abcC12
abcC16
abcD1
abcD2
abcD3
abcE1
abcF1
abcF2
abcF3
abcF4
abcG1
abcG2
abcG3
DPU_G0053610
DPU_G0059808
DPU_G0051826
DPU_G0073960
DPU_G0066722
DPU_G0058190
DPU_G0053338
DPU_G0064134
DPU_G0070874
DPU_G0059914
DPU_G0074414
DPU_G0072486
DPU_G0060990
DPU_G0053626
D. purpureum
Gene I.D.
e_gw1.89.29.1
GID1.0046674
estExt_Genewise1.C_4230003
estExt_fgeneshDP_pm.C_1200013
e_gw1.49.29.1
e_gw1.319.2.1
e_gw1.376.3.1
e_gw1.89.48.1 + e_gw1.89.35.1
GID1.0039219
GID1.0039969
estExt_Genewise1.C_1950002
e_gw1.286.4.1
fgeneshDP_pm.C_scaffold_140000
02
GID1.0042921
fgeneshDP_pg.C_scaffold_3000082
fgeneshDP_pg.C_scaffold_1980000
20
GID1.0040785
estExt_fgeneshDP_pg.C_230043
fgeneshDP_pm.C_scaffold_230000
19
N.A.
GID1.0050317
estExt_Genewise1Plus.C_1400016
GID1.0039677
estExt_Genewise1.C_970030
fgeneshDP_pg.C_scaffold_4700002
3
estExt_Genewise1.C_1310018
GID1.0038880
e_gw1.106.25.1 instead of
GID1.0042473
GID1.0050952
estExt_Genewise1.C_4040012
estExt_Genewise1.C_2080019
estExt_fgeneshDP_pg.C_1280016
GID1.0047706
GID1.0050163
e_gw1.241.22.1
estExt_Genewise1Plus.C_80085
estExt_Genewise1Plus.C_660033
estExt_fgeneshDP_pg.C_2640005
estExt_Genewise1Plus.C_1310032
26
Protein
I.D.
31990
156020
50951
94555
29588
40017
41231
32029
31972
148530
149280
48852
39254
85995
D. discoideum
ortholog
dictyBase
Gene I.D.
abcA1
DDB_G0291994
abcA2
DDB_G0267438
abcA3
DDB_G0293436
abcA4
DDB_G0274121
abcA5
DDB_G0274119
abcA6
DDB_G0291245
abcA8
DDB_G0271138
abcA9
DDB_G0291980
abcB1
abcB2
abcB3
abcB4
abcB5
DDB_G0293416
DDB_G0293438
DDB_G0291714
DDB_G0279915
DDB_G0292554
152232
74128
80697
abcB6
abcB7
none
DDB_G0282931
DDB_G0269720
150096
96674
86237
tagA
tagB
tagC
DDB_G0293002
DDB_G0286119
DDB_G0286121
159691
55519
148988
47315
76449
tagD
abcC2
abcC3
abcC5
abcC8
abcC9
DDB_G0286123
DDB_G0280055
DDB_G0287691
DDB_G0286559
DDB_G0284867
DDB_G0285165
abcC10
abcC12
DDB_G0280977
DDB_G0280973
abcD1
abcD2
abcD3
abcE1
abcF1
abcF2
abcF3
abcF4
abcG1
abcG2
abcG3
DDB_G0279917
DDB_G0293194
DDB_G0279919
DDB_G0290483
DDB_G0285997
DDB_G0284047
DDB_G0275637
DDB_G0267436
DDB_G0269214
DDB_G0275689
DDB_G0287461
47873
148191
32770
151784
160365
50838
48982
97974
157052
159537
37987
52338
54176
98941
55375
abcG4
abcG5
abcG7
abcG8
abcG11
abcG12
abcG14
abcG15
abcG16
abcG17
abcG18
abcG20
abcG21
abcG22
abcG23
abcG24
abcG25
abcG26
abcG27
abcG28
abcG29
abcG30
abcG31
abcG32
abcG33
abcG34
DPU_G0055092
DPU_G0067272
DPU_G0055090
DPU_G0070800
DPU_G0056894
DPU_G0059036
DPU_G0066602
DPU_G0058848
DPU_G0058224
DPU_G0064052
DPU_G0060986
DPU_G0053174
DPU_G0059566
DPU_G0062512
DPU_G0062252
DPU_G0064878
DPU_G0074636
DPU_G0065042
DPU_G0057694
DPU_G0057746
DPU_G0053204
DPU_G0059038
DPU_G0055496
DPU_G0059586
DPU_G0059396
DPU_G0066902
arsA
arsB
DPU_G0056324
DPU_G0067778
abcH1
abcH2
abcH3
abcH4
DPU_G0074228
DPU_G0074244
DPU_G0054400
DPU_G0074876
abcH5
DPU_G0062188
GID1.0043994
estExt_Genewise1.C_4220006
GID1.0043993
estExt_Genewise1Plus.C_570059
GID1.0044821
GID1.0045623
GID1.0039780
GID1.0038770
e_gw1.209.12.1
e_gw1.333.5.1
GID1.0046454
GID1.0043107
GID1.0045860
GID1.0037392
estExt_Genewise1Plus.C_2920005
estExt_Genewise1Plus.C_3560012
gw1.82.6.1
e_gw1.36.6.1
e_gw1.20.4.1
e_gw1.20.35.1
e_gw1.126.15.1
estExt_fgeneshDP_pg.C_2230012
GID1.0044153
GID1.0045870
GID1.0038839
fgeneshDP_pg.C_scaffold_4100002
9
estExt_Genewise1.C_1780012
fgeneshDP_pg.C_scaffold_4400004
8
e_gw1.79.40.1
GID1.0041478
gw1.143.15.1
fgeneshDP_pg.C_scaffold_8500002
0
fgeneshDP_pg.C_scaffold_2900003
9
27
153305
50946
153304
53928
154132
154969
149091
148081
36905
40327
155800
152418
155206
146703
57493
58057
5674
28616
27275
27204
33697
98693
153464
155216
148150
76201
abcG4
abcG5
abcG7
abcG8
abcG11
abcG12
abcG14
abcG15
abcG16
abcG17
abcG18
abcG20
abcG21
abcG22
abcG23
abcG24
none
none
none
none
none
none
DDB_G0289657
DDB_G0281391
DDB_G0289655
DDB_G0274117
DDB_G0269212
DDB_G0274115
DDB_G0269210
DDB_G0267432
DDB_G0289331
DDB_G0273073
DDB_G0275687
DDB_G0267430
DDB_G0269206
DDB_G0270826
DDB_G0269026
DDB_G0282103
48651
76346
arsA
arsB
DDB_G0293528
DDB_G0289879
31462
150789
15107
77869
abcH1
abcH2
abcH3
abcH4
DDB_G0292384
DDB_G0267428
DDB_G0275697
DDB_G0283479
75661
none
28
29
30
Figure S10. ABC transporter genes of D. purpureum and D. discoideum. Dendrograms of the
families of ABC proteins from the D. discoideum and D. purpureum genomes.
Protein kinases
D. purpureum has a similar complement of protein kinases as compared to D. discoideum. There
are 262 eukaryotic protein kinases (ePKs; having at least one ePK domain, IPR000719) and 41
atypical protein kinases (aPKs) that are listed in Table S9. The main groups of protein kinases
are separated by grey bars, and families within those groups are roughly indicated by various
colors. The aPK groups are each colored differently and also separated by grey bars.
31
Table S9. The protein kinases of D. purpureum and D discoideum. Grey bars indicate major divisions
in protein kinase groups (ePK, unclassified, atypical) and colored blocks roughly divide the predicted
genes/proteins into protein kinase subfamilies.
Eukaryotic Protein Kinases (ePK)
D. purpureum
dictyBase Gene
Protein
Proposed
I.D.
I.D.
Gene Name
DPU_G0068090
42383
pkaC
Closest paralog
dictyBase Gene
I.D.
DDB_G0283907
DPU_G0058066
8174
pkaD
DDB_G0277145
DPU_G0072818
100116
pkgD
DDB_G0284029
DPU_G0061370
DPU_G0053200
DPU_G0068224
38849
152431
149347
pkbA1
pkbA2
DDB_G0268620
DDB_G0268620
DDB_G0288795
DPU_G0071804
159783
pkgA
DDB_G0276157
DPU_G0064080
50356
DDB_G0272282
DPU_G0054528
34584
DDB_G0293276
DPU_G0064200
50393
drA
DDB_G0278457
DPU_G0070842
51572
ndrB
DDB_G0288753
DPU_G0074558
87338
DDB_G0278845
DPU_G0053304
92065
DDB_G0290859
DPU_G0058964
56680
pdkA
DDB_G0281471
DPU_G0056736
36122
pdkB
DDB_G0284489
DPU_G0060130
98847
DDB_G0290157
DPU_G0062384
39515
DDB_G0277449
DPU_G0069160
58802
snfA
DDB_G0277905
DPU_G0072054
90836
prkag
DDB_G0272542
DPU_G0064894
157371
mrkB
DDB_G0285643
DPU_G0058454
154713
mrkC
DDB_G0281895
DPU_G0064378
DPU_G0072942
99342
150403
fhkA
(DDB_G0281895)
DDB_G0293656
DPU_G0064488
157188
fhkC
DDB_G0281567
32
D. discoideum
Closest paralog
Description from annotation (modified
Name
to be consistent with the predicted D.
purpureum protein)
pkaC
cAMP-dependent protein kinase, AGC
group
pkaD
cAMP-dependent protein kinase, AGC
group
pkgD
cAMP-dependent protein kinase, AGC
group
pkbA
AKT/PKB protein kinase, AGC group
pkbA
AKT/PKB protein kinase, AGC group
DDB_G0288795
AKT family protein kinase, AGC
group
pkgA
MAST family protein kinase, AGC
group
DDB_G0272282
MAST family protein kinase, AGC
group
DDB_G0293276
MAST family protein kinase, AGC
group
ndrA
NDR family protein kinase, AGC
group
ndrB
NDR family protein kinase, AGC
group
DDB_G0278845
NDR family protein kinase, AGC
group
DDB_G0290859
NDR family protein kinase, AGC
group
pdkA
PDK1 family protein kinase, AGC
group
pdkB
PDK1 family protein kinase, AGC
group
pkgB
SGK family protein kinase, AGC
group
DDB_G0277449
SGK family protein kinase, AGC
group
snfA
AMP-activated protein kinase alpha
subunit, A (AMPK), CAMK group
prkag
AMP-activated protein kinase gamma
subunit (AMPK), CBS (cystathioninebeta-synthase) domain
mrkB
similar to SNF1 kinases, MARK
kinases, and AMPK kinases
mrkC
similar to MARK kinases, SNF1
kinases, and AMPK kinases
(mrkC)
very weak similarity to MARK kinases
fhkA
FHA domain-containing protein,
RAD53 family protein kinase, CAMK
group
fhkC
FHA domain-containing
protein,similar to mammalian chk2 and
yeast RAD53
DPU_G0060718
38535
fhkD
DDB_G0285963
fhkD
DPU_G0066926
29047
fhkE
DDB_G0280321
fhkE
DPU_G0074230
47007
lkb1
DDB_G0279629
lkb1
DPU_G0066302
157928
mlkA
DDB_G0279925
mlkA
DPU_G0074364
52310
DDB_G0275057
DDB_G0275057
DPU_G0058438
49032
DDB_G0282429
DDB_G0282429
DPU_G0064206
95599
DDB_G0292624
DDB_G0292624
DPU_G0059860
37955
DDB_G0271550
DDB_G0271550
DPU_G0070118
51418
mrkA
DDB_G0292304
mrkA
DPU_G0061116
DPU_G0063552
57246
148677
pXi
DDB_G0289119
DDB_G0279405
pXi
DDB_G0279405
DPU_G0066846
DPU_G0071624
DPU_G0051654
76173
59197
151676
DDB_G0279831
DDB_G0284661
DDB_G0280133
DDB_G0279831
DDB_G0284661
DDB_G0280133
DPU_G0060118
49516
DDB_G0277165
DDB_G0277165
DPU_G0064538
50476
DDB_G0292354
DDB_G0292354
DPU_G0064746
50512
DDB_G0273737
DDB_G0273737
DPU_G0069324
96328
glkA
DDB_G0270218
glkA
DPU_G0052036
26270
casK
DDB_G0276885
casK
DPU_G0072090
43974
DDB_G0286481
DDB_G0286481
DPU_G0064536
40649
clkA
DDB_G0281179
clkA
DPU_G0067960
91498
sky1
sky1
(DDB_G0275627)
DDB_G0274613
DDB_G0274613
DPU_G0058602
98641
DPU_G0067110
41903
cdk1
DDB_G0272813
cdk1
DPU_G0064348
92862
cdk5
DDB_G0288677
cdk5
DPU_G0067682
29225
cdk7
DDB_G0285417
cdk7
DPU_G0068446
58676
cdk8
DDB_G0267442
cdk8
DPU_G0064748
157293
cdk9
DDB_G0273207
cdk9-1
DPU_G0053558
18522
cdk10
DDB_G0268480
cdk10
33
FHA domain-containing protein,
RAD53 family protein kinase, CAMK
group
FHA domain-containing protein,
RAD53 family protein kinase, CAMK
group
CAMKL family, LKB subfamily
protein kinase, CAMK group
CAMK1 family, phosphorylates
myosin II regulatory light chain at S13
CAMK1 family, CAMK group,
putative myosin light chain kinase
CAMK1 family, CAMK group,
putative myosin light chain kinase
CAMK1 family, CAMK group,
putative myosin light chain kinase
CAMK1 family, CAMK group,
putative myosin light chain kinase
CAMKL family, MARK subfamily
protein kinase, CAMK group
CAMK1 family, CAMK group
CAMKK family, Meta subfamily
protein kinase
CAMK1 family, CAMK group
CAMK1 family, CAMK group
CAMKL family, QIK subfamily
protein kinase, CAMK group
CAMKL family, BRSK subfamily,
CAMK group
TTBK family protein kinase, CK1
group, putative casein kinase I,
putative tau-tubulin kinase
Similar to Dictyostelium discoideum
casein kinase 1, CK1 group
GSK family protein kinase, CMGC
group
CK2 family protein kinase, casein
kinase II alpha chain, CMGC group
CK2 family protein kinase, CMGC
group, putative casein kinase II alpha
chain (CK2)
CLK family protein kinase, CMGC
group
SRPK family protein kinase, CMGC
group
RING zinc finger-containing protein,
CMGC group
CDC2 subfamily protein kinase, CDK
family protein kinase, p34-cdc2
protein, CMGC group
CDK family cyclin-dependent kinase,
CMGC group
CDK family cyclin-dependent kinase,
p34-cdc2 protein, CMGC group
CDK family cyclin-dependent kinase,
CMGC group
similar cdc2-related protein kinase 7
(CRK7) and other cell division cycle 2like protein kinases
cell division cycle 2 (CDC2)-like
DPU_G0071398
74328
cdk11
DDB_G0283279
DPU_G0074212
160441
DDB_G0274007
DPU_G0068044
42322
DDB_G0278487
DDB_G0278487
DPU_G0059916
155330
cdc7
DDB_G0292152
cdc7
DPU_G0057164
154263
mps1
DDB_G0280995
mps1
DPU_G0060506
38421
bub1
DDB_G0292676
bub1
DPU_G0063456
156778
rio2
DDB_G0282099
rio2
DPU_G0063564
DPU_G0071982
96852
24715
aurK
nek3
DDB_G0279343
DDB_G0275241
aurK
nek3
DPU_G0073774
44395
DDB_G0283927
DDB_G0283927
DPU_G0057408
154392
DDB_G0270444
DDB_G0270444
DPU_G0069580
97131
yakA
DDB_G0283605
yakA
DPU_G0051834
97778
dyrk1
DDB_G0277485
dyrk1
DPU_G0051982
91968
dyrk2
DDB_G0293750
dyrk2
DPU_G0071516
54020
prpf4B
DDB_G0279703
prpf4B
DPU_G0057548
146611
fnkA
DDB_G0275561
fnkA
DPU_G0053468
74778
(DDB_G0275561)
DPU_G0066830
158080
(DDB_G0275561)
DPU_G0066832
158081
(DDB_G0275561)
DPU_G0051700
47438
fnkB
DDB_G0267934
fnkB
DPU_G0055908
147757
fnkC
DDB_G0276349
fnkC
DPU_G0063898
DPU_G0053466
75824
147525
fnkD
fnkE
(DDB_G0273129)
DDB_G0275879
fnkD
fnkE
DPU_G0053464
74775
(DDB_G0275879)
DPU_G0057098
98488
(DDB_G0275879)
DPU_G0054654
34641
(DDB_G0275879)
DPU_G0062608
146753
(DDB_G0275879)
DPU_G0054652
34650
(DDB_G0275879)
34
cdk11
protein kinase; has similarity to
PITSLRE proteins and other CDK2s
CDK family cyclin-dependent kinase,
CMGC group
similar to cyclin dependent protein
kinases, CMGC group
CDK family protein kinase, CMGC
group
similar to S. cerevisiae cell division
control protein 7 (CDC7), a S/T kinase
required for mitosis and meiosis
similar to yeast and zebrafish mps1
(monopolar spindle) kinase, a
threonine/tyrosine kinase
BUB family protein kinase, putative
mitotic checkpoint protein
contains RIO1 domain; winged helix
DNA-binding domain; RIO1 plays a
role in cell cycle progression
Aurora family protein kinase
NEK family protein kinase, putative
protein serine/threonine kinase
NEK family protein kinase, putative
protein serine/threonine kinase
similar to MAPK, D.d. lacks resdiues
required for kinase function; contains
WD40 repeats, CMGC group
DYRK family protein kinase, CMGC
group
DYRK family protein kinase, CMGC
group
DYRK family protein kinase, CMGC
group
DYRK family protein kinase, PRP4 pre-mRNA processing factor 4
homolog B, CMGC group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein,kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP containing protein kinase
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
DPU_G0053462
147523
(DDB_G0275879)
DPU_G0053448
147516
(DDB_G0275879)
DPU_G0069014
149485
(DDB_G0275879)
DPU_G0061836
49896
mkkA
DDB_G0283265
mkkA
57414
mkkB
(DDB_G0283265)
(mkkA)
DPU_G0061140
155882
(DDB_G0283265)
(mkkA)
DPU_G0072542
160010
(DDB_G0283265)
(mkkA)
DPU_G0074488
150832
dst1
DDB_G0274593
dst1
DPU_G0055740
153614
dst3
DDB_G0291267
dst3
DPU_G0066164
83651
dst4
DDB_G0288071
dst4
DPU_G0052246
33056
DDB_G0278901
DDB_G0278901
DPU_G0051338
91138
fray1
DDB_G0278863
fray1
DPU_G0060884
57173
fray2
DDB_G0276577
fray2
DPU_G0058244
96609
sepA
DDB_G0276465
sepA
DPU_G0061144
38722
(DDB_G0276465)
(sepA)
DPU_G0062510
96263
pakA
DDB_G0269166
pakA
DPU_G0074072
31335
pakB
DDB_G0276459
pakB
DPU_G0074390
91113
pakC
DDB_G0267450
pakC
DPU_G0059930
155336
pakD
DDB_G0269696
pakD
DPU_G0072662
44150
pakE
DDB_G0293932
pakE
DPU_G0074510
150846
pakF
DDB_G0274409
pakF
DPU_G0056426
147802
pakG
DDB_G0282891
pakG
DPU_G0064392
157139
(DDB_G0282891)
(pakG)
DPU_G0065958
90051
pakH
DDB_G0273865
pakH
DPU_G0061606
92678
svkA
DDB_G0286359
svkA
DPU_G0052716
93521
krsA
DDB_G0284181
krsA
35
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
FNIP repeat-containing protein kinase,
STE group
F-box MEK kinase, STE11 family
protein kinase, WD40 repeat,
octicosapeptide/Phox/Bem1p domain
F-box MEK kinase, STE11 family
protein kinase, WD40 repeat, D.p.
protein highly similar to mkkA
weak similarity to DDB_G0283265
(mkkA)
weak similarity to DDB_G0283265
(mkkA)
similar to mammalian STK3 and STK4
(MST) kinases
similar to mammalian STK3 and STK4
(MST) kinases, and other STE20-like
kinases
STE20 family protein kinase, protein
kinase, STE group
STE group, putative protein
serine/threonine kinase
FRAY subfamily, STE20 family, STE
group
FRAY subfamily, STE20 family, STE
group
armadillo repeat-containing protein,
STE group, septase
STE group septase (Possible
pseudogene)
PAKA subfamily, STE20 family
protein kinase, p21-activated protein
kinase, STE group
PAKA subfamily, STE20 family
protein kinase, myosin I heavy chain
kinase, p21-activated protein kinase
PAKA subfamily, STE20 family
protein kinase, PH domain, STE group
similar to D.d. pakA (Ste20/PAK
family); putative p21-activated kinase;
calponin-like actin-binding domain
PAKL subfamily protein kinase,
STE20 family protein kinase, protein
kinase, STE group
similar to mammalian STK3 and STK4
(MST) kinases
PAKL subfamily protein kinase,
STE20 family protein kinase, STE
group
similar to mammalian STK3 and STK4
(MST) kinases, and other STE20-like
kinases
PAKL subfamily protein kinase,
STE20 family protein kinase, STE
group
STE20 family protein kinase, YST
subfamily, STE group, severin kinase
STE group, MST subfamily kinase,
DPU_G0054724
93560
krsB
DDB_G0267978
krsB
DPU_G0058304
93640
dst2
DDB_G0267730
dst2
DPU_G0059330
148117
mkcA
DDB_G0285427
mkcA
DPU_G0068038
158544
mkcB
DDB_G0290723
mkcB
DPU_G0052150
151903
mkcC
DDB_G0287853
mkcC
DPU_G0059750
95210
mkcD
DDB_G0277413
mkcD
DPU_G0070094
96000
mkcE
DDB_G0281649
mkcE
DPU_G0057256
154313
mkcF
DDB_G0270102
mkcF
DPU_G0068018
53558
erkA
DDB_G0286353
erkA
DPU_G0063478
93783
erkB
DDB_G0283903
erkB
DPU_G0060050
98833
DDB_G0269152
mekA
DPU_G0069236
52129
DDB_G0293124
kxcB
DPU_G0062136
96792
DDB_G0293184
DDB_G0293184
DPU_G0070478
90653
DDB_G0270146
DDB_G0270146
DPU_G0063436
95528
DDB_G0284251
DDB_G0284251
DPU_G0072724
96158
DDB_G0292350
DDB_G0292350
DPU_G0054990
48249
DDB_G0283821
DDB_G0283821
DPU_G0051704
78437
DDB_G0268550
DDB_G0268550
DPU_G0051702
78436
(DDB_G0268550)
DPU_G0062518
146705
(DDB_G0276187)
(pyk4)
DPU_G0074738
77798
(DDB_G0276187)
(pyk4)
DPU_G0054656
98147
ifkB
DDB_G0276829
ifkB
DPU_G0068358
158682
ifkC
DDB_G0276043
ifkC
DPU_G0073386
160208
DDB_G0268642
DPU_G0065112
9913
DDB_G0292734
DPU_G0064512
83097
DDB_G0283065
DPU_G0054406
98108
DDB_G0268642
kxcB
36
DDB_G0283065
STE20 family, krs1-like kinase, protein
serine/threonine kinase
STE group, MST subfamily kinase,
STE20 family, calpain-like cysteine
protease, peptidase C2 family protein
STE20 family protein kinase, STE
group
MKC subfamily, STE20 family protein
kinase, STE group
MKC subfamily, STE20 family protein
kinase, STE group
MKC subfamily, STE20 family protein
kinase, STE group
MKC subfamily, STE20 family protein
kinase, STE group
MKC subfamily, STE20 family protein
kinase, STE group
MKC subfamily, STE20 family protein
kinase, STE group
ERK subfamily, MAPK family protein
kinase
ERK subfamily, MAPK family protein
kinase
MAP kinase kinase (MAP2K), STE7
family protein kinase, STE group
DH and PH domain-containing protein,
RhoGEF domain-containing protein,
STE group
RhoGAP domain-containing protein,
STE group
STE group, putative protein
serine/threonine kinase
STE group, putative protein
serine/threonine kinase
STE group, putative protein
serine/threonine kinase
STE group, putative protein
serine/threonine kinase
STE group, putative protein
serine/threonine kinase
STE group STE20 family (Possible
fragment of 78437 above)
N-terminal kinase domain related to
STE group
N-terminal kinase domain related to
STE group
GCN2 subfamily protein kinase, PEK
family protein, putative eIF2alpha
kinase
GCN2 subfamily protein kinase, PEK
family protein, putative eIF2alpha
kinase
related to GCN2 family; it does not
contain a catalytic aspartate
related to GCN2 family of protein
kinases
PEK family protein kinase, putative
eIF2alpha kinase
related to GCN2 family; unlikely to
function as a kinase- no catalytic
aspartate
DPU_G0075598
78158
irlC
DDB_G0270894
irlC
DPU_G0057530
96238
DPU_G0061794
92689
DPU_G0057530
96238
DPU_G0057562
96243
irlD
(DDB_G0270894)
DDB_G0269632
irlD
DPU_G0069426
58819
ireA
DDB_G0267650
ireA
DPU_G0051864
78515
DDB_G0291350
DDB_G0291350
DPU_G0055080
98203
DDB_G0276461
DDB_G0276461
DPU_G0065850
95721
DDB_G0280111
DDB_G0280111
DPU_G0070418
94041
tsuA
DDB_G0267962
tsuA
DPU_G0069554
159087
atg1
DDB_G0292390
atg1
DPU_G0071576
51646
cct3
DDB_G0281741
cct3
DPU_G0053554
55347
scy1
DDB_G0267540
scy1
DPU_G0067502
158338
scy2
DDB_G0270808
scy2
DPU_G0055694
153587
vps15
DDB_G0282627
vps15
DPU_G0056214
153832
DDB_G0276527
DDB_G0276527
DPU_G0054788
79620
slob1
DDB_G0281863
slob1
DPU_G0058362
DPU_G0062732
DPU_G0063474
75243
75685
82742
slob2
DDB_G0279303
(DDB_G0277989)
DDB_G0267760
slob2
DPU_G0055504
98258
DDB_G0274503
PLK
DPU_G0057080
98486
DDB_G0277071
DDB_G0277071
DPU_G0073194
150424
DDB_G0291436
DDB_G0291436
DPU_G0075140
DPU_G0071390
74505
147000
(DDB_G0277989)
DDB_G0283109
iksA
(DDB_G0270894)
(DDB_G0270894)
tbck
iksA
37
IRE family the kinase domain is
similar to yeast IRE1 kinase required
for inositol phototroph
IRE family protein kinase
IRE family protein kinase similar to
yeast IRE1 kinase required for inositol
phototrophy; contains SWIM Zn-finger
IRE family protein kinase
tbck
IRE1 kinase required for inositol
phototrophy
IRE family protein kinase, putative
endoribonuclease
NAK (Numb-associated kinase) family
protein kinase, putative MPSK
NAK family protein kinase, putative
protein serine/threonine kinase
NAK family protein kinase, putative
protein serine/threonine kinase
ULK family protein kinase, fused-like
protein kinase, putative protein
serine/threonine kinase
Dictyostelium homolog of yeast atg1,
belongs to the ULK (Unc-51-like
kinase) family of kinases; required for
macroautophagy
chaperonin containing TCP1 gamma
subunit
SCY1 family encodes highly
conserved non-canonical kinases that
are believed to function
SCY1 family encodes highly
conserved non-canonical kinases that
are believed to function
similar to human PIK3R4 and yeast
VPS15, which regulate VPS34
(hVps34); known to be involved in
vacuolar protein sorting
putative protein containing 3 major
domains: one RCC1 domain, one
protein kinase domain, and one HECT
domain
Slob family protein kinase, FVYE and
WH2 domains
Slob family protein kinase
Two ser/thr kinase domains
RabGAP/TBC domain-containing
protein, TBCK family protein kinase
polo family protein kinase, putative
protein serine/threonine kinase
putative protein tyrosine phosphatase,
dual specificity
Q86SQ9 Dehydrodolichyl diphosphate
synthase (Dedol-PP synthase).
Similarity to D.d. not in the kinase
domain of the D.p. protein.
contains two kinase domains
IKS family protein kinase, IQ
calmodulin-binding domain, putative
transmembrane protein
DPU_G0051978 97806
Tyrosine Kinase like
DPU_G0075364 91861
DDB_G0293746
DDB_G0293746
kinase motif-containing (KMC) protein
arkA
(DDB_G0289555)
arkA
phg2
DDB_G0283699
phg2
82991
DDB_G0282963
DDB_G0282963
DPU_G0065390
148930
DDB_G0290471
DDB_G0290471
DPU_G0064056
95570
DDB_G0273531
spkA-2
DPU_G0058284
75207
DDB_G0267686
DDB_G0267686
DPU_G0070650
43457
DDB_G0272092
DDB_G0272092
DPU_G0056958
16456
DDB_G0278535
DPU_G0063252
99201
DDB_G0278521
DPU_G0058188
8978
DDB_G0271682
DPU_G0051656
78414
DDB_G0280131
DDB_G0280131
DPU_G0051314
147302
DDB_G0278909
DDB_G0278909
DPU_G0068520
53617
DDB_G0283385
splA
DPU_G0061764
91361
(DDB_G0283385)
(splA)
DPU_G0065758
92958
(DDB_G0283385)
(splA)
DPU_G0074712
19597
(DDB_G0283385)
(splA)
DPU_G0058658
56632
DDB_G0285321
splB
DPU_G0066514
25407
(DDB_G0276025)
DPU_G0051780
78473
(DDB_G0276025)
DPU_G0073450
46831
(DDB_G0276025)
DPU_G0063812
40205
DDB_G0285463
DDB_G0285463
DPU_G0064800
4928
DDB_G0283397
DDB_G0283397
ARK (ankyrin repeat-containing
kinase) family, suppressor of spalten
(spnA) mutant; member of the TKL
(tyrosine kinase-like) group
ARK family protein kinase, TKL
group
ARK family protein kinase, TKL
group
ARK family protein kinase, TKL
group, tyrosine kinase-like protein
ARK family protein kinase, SAM
domain-containing protein, TKL
group, stress-activated MEK-like
kinase
ARK family protein kinase, RGS
domain-containing protein, protein
kinase, TKL group
ARK family protein kinase, C2
domain-containing protein, SAM
domain-containing protein, TKL group
ARK family protein kinase; SAM
(Sterile alpha motif) domain, TKL
group
HH498 subfamily protein kinase, MLK
family protein kinase, TKL group
member of the TKL group; belongs to
the ARK (ankyrin repeat-containing
kinase) family, although it does not
contain ankyrin repeats
ARMK family protein kinase,
armadillo repeat-containing protein,
TKL group
ARMK family protein kinase,
armadillo repeat-containing protein,
leucine-rich repeats (LRR), TKL group
CZAK (C-terminal domain of ZakA)
family protein kinase, dual-specificity
protein kinase, TKL group
CZAK (C-terminal domain of ZakA)
family protein kinase, dual-specificity
protein kinase, TKL group
CZAK (C-terminal domain of ZakA)
family protein kinase, dual-specificity
protein kinase, TKL group
weak similarity to splA, CZAK,
member of the TKL group
CZAK (C-terminal domain of ZakA)
family, TKL group
kinase domain similar to TKL group
zakA
kinase domain similar to TKL group
zakA
kinase domain similar to TKL group
zakA
kinase domain similar to TKL group
zakA, putative transmembrane protein,
tyrosine kinase-like protein
kinase domain similar to TKL group
zakA
DPU_G0051824
32789
DPU_G0064186
spkA-2
splA
splB
38
DDB_G0278521
DPU_G0073902
10036
DPU_G0071248
100013
DPU_G0075472
91876
DPU_G0069888
159186
DPU_G0064592
157247
DPU_G0066438
25383
DPU_G0052888
33484
DPU_G0072350
(DDB_G0283397)
pkyA
DDB_G0289001
pkyA
(DDB_G0289001)
(pykA)
DDB_G0289709
drkB
(DDB_G0289709)
(drkB)
drkC
DDB_G0281899
drkC
drkD
DDB_G0281557
drkD
97331
DDB_G0270544
gdt6
DPU_G0072354
77168
DDB_G0278879
gdt9
DPU_G0065986
157827
kxcA
DDB_G0289859
kxcA
DPU_G0066732
41714
kinX
DDB_G0283391
kinX
DPU_G0061012
155812
DDB_G0289661
kinY
DPU_G0053516
152543
DDB_G0271538
DDB_G0271538
DPU_G0053790
152685
DDB_G0269298
gefX
DPU_G0071580
159703
DDB_G0281745
DPU_G0069360
149540
DDB_G0275165
DDB_G0275165
DPU_G0059584
49348
DDB_G0280461
DDB_G0280461
DPU_G0069936
99895
DDB_G0271402
DDB_G0271402
DPU_G0066116
99535
DDB_G0282895
DDB_G0282895
DPU_G0071386
96342
DDB_G0283267
shkA
DPU_G0067818
158466
DDB_G0288617
shkB
DPU_G0054978
55744
shkC
DDB_G0278409
shkC
DPU_G0071724
159737
shkE
DDB_G0290451
shkE
DPU_G0061708
148427
rckA
pats1
drkB
gefX
shkA
(shkE)
DPU_G0052914
152279
rckA
(DDB_G0290451)
DDB_G0278737
DPU_G0070698
159478
pats1
DDB_G0269250
39
weak similarity to DDB_G0283397,
member of the TKL (tyrosine kinaselike) group and the CZAK (C-terminal
domain of ZakA) family
DPYK family protein kinase, TKL
group
DPYK family protein kinase, TKL
group
DRK (Dictyostelium receptor-like
kinase) subfamily, TKL group
DRK (Dictyostelium receptor-like
kinase) subfamily, TKL group
DRK subfamily protein kinase, E set
domain-containing protein, TKL grop
DRK subfamily protein kinase,
leucine-rich repeats (LRR), TKL group
GDT family protein kinase, TKL
group, putative transmembrane protein
GDT family protein kinase, TKL
group, putative transmembrane protein
LISK (LIM domain and testis-specific
kinase) family; contains calmodulinbinding, RhoGEFand PH domains
LISK (LIM domain and testis-specific
kinase) family protein kinase, TKL
group
LISK family; similar to LIM kinases
which regulate actin dynamics, TKL
group
LISK (LIM domain and testis-specific
kinase) family; expressed in pstO cells,
TKL group
LISK (LIM domain and testis-specific
kinase) family; RasGEF nucleotide
exchange factor domain, TKL group
LISK (LIM domain and testis-specific
kinase) family, TKL group
LISK family protein kinase, TKL
group
LISK family protein kinase, TKL
group
LISK family protein kinase, TKL
group
MORN repeat-containing protein, TKL
group
SH2 domain-containing protein, SHK
subfamily protein kinase, TKL group
SH2 domain-containing protein, SHK
subfamily protein kinase, TKL group
SH2 domain-containing protein, SHK
subfamily protein kinase, TKL group
SH2 domain-containing protein, SHK
subfamily protein kinase, TKL group,
contains a C-terminal SH2 (Src
homology 2) domain
SH2 domain-containing protein, SHK
subfamily protein kinase, TKL group
RGS (Regulator of G protein
Signaling) domain, TKL group
ROCO family protein kinases; contains
LRR, Roc, COR, WD40 domains,
DPU_G0059624
95196
gbpC
DDB_G0291079
gbpC
DPU_G0058498
49056
roco4
DDB_G0288251
roco4
DPU_G0063182
148631
roco5
DDB_G0294533
roco5
DPU_G0065240
95686
roco6
DDB_G0279417
roco6
DPU_G0059300
81310
roco7
DDB_G0267472
roco7
DPU_G0058976
98684
roco8
DDB_G0286127
roco8
DPU_G0072160
150174
DDB_G0288183
roco9
DPU_G0063892
148693
DDB_G0291710
roco10
DPU_G0051594
91930
DDB_G0287001
DDB_G0287001
DPU_G0054076
DPU_G0053128
147550
152395
DDB_G0278509
DDB_G0288147
DDB_G0278509
DDB_G0288147
DPU_G0055048
79745
DDB_G0276181
DPU_G0070696
DPU_G0056114
96054
94884
DDB_G0267514
DDB_G0272254
DDB_G0267514
DDB_G0272254
DPU_G0072288
DPU_G0060552
87059
38450
DDB_G0278665
DDB_G0268876
DDB_G0278665
DDB_G0268876
DPU_G0057092
154223
DDB_G0290621
DPU_G0068556
29443
DDB_G0291842
DDB_G0291842
DPU_G0058790
148051
DDB_G0277539
DDB_G0277539
DPU_G0068882
158867
DDB_G0291133
DDB_G0291133
Unclassified kinases and proteins with weak similarity to characterized kinases.
DPU_G0072986 160136
DDB_G0277989
DDB_G0277989
DPU_G0067288 41971
DDB_G0271366
DDB_G0271366
DPU_G0060500 155584
(DDB_G0277989)
DPU_G0066578 53438
DDB_G0269628
DDB_G0269628
DPU_G0053258 79056
DDB_G0293958
DDB_G0293958
DPU_G0072554 51786
DDB_G0279719
DDB_G0279719
DPU_G0075162 147224
DDB_G0293292
DDB_G0293292
DPU_G0063940 96861
DDB_G0291918
DDB_G0291918
DPU_G0053292 33770
DDB_G0281331
DDB_G0281331
40
TKL group
RasGEF domain-containing protein,
cyclic GMP-binding protein, leucinerich repeats (LRR), TKL group
ROCO family protein kinase, leucinerich repeats(LRR), TKL group
ROCO family protein kinase, RhoGEF
domain, leucine-rich repeats (LRR),
PH domain, TKL group
ROCO family protein kinase, leucinerich repeats (LRR), PH domain, TKL
group
ROCO family protein kinase, WD40
repeat-containing protein, TKL group
ROCO family protein kinase, leucinerich repeats (LRR), DEP domain, TKL
group
ROCO family protein kinase, RhoGAP
domain, leucine-rich repeats (LRR),
TKL group
ROCO family protein kinase,
RhoGAP, RGS, Kelch domaincontaining protein, leucine-rich repeats
(LRR), TKL group
LIM-type zinc finger-containing
protein, TKL group
protein kinase, TKL group
similar to plant serine/threonine
kinases; contains a phorbol
ester/diacylglycerol-binding domain,
TKL group
TKL group of protein kinases; contains
a PH (pleckstrin homology) domain
TKL group
TKL group, Kelch repeat-containing
protein, galactose oxidase domaincontaining protein
TKL group
filamin/ABP280 repeat-containing
protein, protein kinase,TKL group
member of the TKL group of protein
kinases
WEE1 family protein kinase, putative
protein tyrosine kinase
WEE1 family protein kinase, putative
protein tyrosine kinase
similar to S. pombe wee1, inhibitor of
mitosis through phosphorylation of
cdc2
putative kinase
putative kinase
putative protein serine/threonine kinase
putative protein serine/threonine kinase
putative protein serine/threonine kinase
putative protein serine/threonine kinase
putative protein serine/threonine kinase
putative protein serine/threonine kinase
putative protein serine/threonine
kinase, putative transmembrane protein
DPU_G0056750
DPU_G0051972
36123
151859
DPU_G0067366
42055
DPU_G0068318
158653
DDB_G0274821
DPU_G0053256
DPU_G0058714
DPU_G0058712
DPU_G0074516
79055
81086
154850
160477
Not Identified
Not Identified
Not Identified
Not Identified
DPU_G0058100
DPU_G0072540
DPU_G0067570
9742
160009
13537
Not Identified
Not Identified
Not Identified
DPU_G0073256
DPU_G0061138
160171
155881
Not Identified
Not Identified
DPU_G0058098
154589
Not Identified
DPU_G0058102
154592
Not Identified
DPU_G0066626
DPU_G0068098
DPU_G0073686
157967
158581
150586
Not Identified
Not Identified
Not Identified
DPU_G0073198
150426
Not Identified
DPU_G0073674
77467
Not Identified
DPU_G0071050
85033
Not Identified
DPU_G0069498
84604
Not Identified
DPU_G0070004
76697
Not Identified
DPU_G0057808
27259
Not Identified
DPU_G0064382
83033
Not Identified
Atypical Kinases
D. purpureum
I.D.
Protein
I.D.
DPU_G0055828
DPU_G0071678
pan3
DDB_G0284491
(DDB_G0279945)
DDB_G0284491
DDB_G0279129
pan3
Serine/threonine protein kinase
DDB_G0279945 Closest paralog in D.
discoideum does not encode a kinase
domain
ortholog of PAN3, a member of
poly(A)-ribonuclease complex controls
poly(A) tail; no catalytic aspartate
very weak similarity to Nek kinases
very weak similarity to Nek kinases
very weak similarity to Nek kinases
weak similarity to DDB_G0283391
LISK family protein kinase
weak similarity to DDB_G0270146
weak similarity to DDB_G0278901.
weak similarity to Oryza sativa PK,
XP_482452i
weak similarity to Vibrio S/T kinase
apnB (DDB_G0277247) has similarity
to the C-terminus (non-kinase) of this
protein
XP_445391 unnamed protein product
[Candida glabrata]
CAA42788 ssp31 protein kinase S.
cerevisiae
weak hit to E. histolitica P. kinase
weak hit to E. histolitica P. kinase
YP_643722.1| serine/threonine protein
kinase [Rubrobacter xylanophilus
DSM 9941]
(XP_653371. protein kinase
[Entamoeba histolytica HM-1:IMSS].)
(XP_824253.1. Protein kinase
Trypanosome brucei.)
(XP_450193. putative
serine/threonine-protein kinase ctr1
[Oryza sativa].)
CAJ09507 protein kinase, putative
[Leishmania major].)
(XP_725148 hypothetical protein
[Plasmodium yoelii yoelii str.
17XNL].)
(BAD28399 putative MAP3K alpha 1
protein kinase [Oryza sativa Japonica
Group].
(XP_727189. calcium-dependent
protein kinase [Plasmodium yoelii])
D. discoideum
I.D.
D. discoideum
ortholog
Description from D. discoideum
153663
D.
purpureum
name
dhkA
DDB_G0280961
dhkA
150045
dhkB
DDB_G0277845
dhkB
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
41
DPU_G0066966
158106
dhkC
DDB_G0274191
dhkC
DPU_G0053234
152450
dhkD
DDB_G0282289
dhkD
DPU_G0060290
148245
dhkE
DDB_G0269204
dhkE
DPU_G0069672
51346
dhkF
DDB_G0276143
dhkF
DPU_G0059448
155144
dhkG
DDB_G0284045
dhkG
DPU_G0051968
151857
dhkH
DDB_G0279913
dhkH
DPU_G0064064
157014
dhkI
DDB_G0273475
dhkI
DPU_G0055632
35308
dhkJ
DDB_G0277883
dhkJ
DPU_G0067300
50957
dhkK
DDB_G0277887
dhkK
DPU_G0067586
42128
dhkL
DDB_G0282927
dhkL
DPU_G0059468
155154
dhkM
DDB_G0282377
dhkM
DPU_G0063058
156601
dokA
DDB_G0274101
dokA
DPU_G0054288
34378
vwkA
DDB_G0268144
vwkA
DPU_G0054290
79436
vwkB
DDB_G0268144
(vwkA)
DPU_G0059918
98812
ak1
DDB_G0292150
ak1
DPU_G0063328
95520
mhkD
DDB_G0282489
mhkD
DPU_G0073190
94172
mhkA
DDB_G0291231
mhkA
DPU_G0056802
48766
mhkB
DDB_G0289115
mhkB
DPU_G0070676
51532
mhkC
DDB_G0290687
mhkC
DPU_G0065756
83521
DPU_G0070838
159516
abkA
DDB_G0288749
abkA
DPU_G0066890
16409
abkB
DDB_G0281799
abkB
DPU_G0065070
83271
abkC
DDB_G0267774
abkC
DPU_G0069658
DPU_G0062264
42973
7275
Not Identified
DDB_G0268748
(DDB_G0268748)
DDB_G0268748
DPU_G0065292
99462
Not Identified
(DDB_G0268748)
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
HisK family protein kinase, histidine
kinase
Alpha kinase family, type A von
Willebrand factor (VWFA) domain
protein
Alpha kinase family, type A von
Willebrand factor (VWFA) domain
protein
Alpha kinase family, Arf GTPase
activating protein
Alpha kinase family, MHCK
subfamily protein kinase
Alpha kinase family, MHCK
subfamily protein kinase, myosin
heavy chain kinase
Alpha kinase family, MHCK
subfamily protein kinase, myosin
heavy chain kinase
Alpha kinase family, MHCK
subfamily protein kinase, myosin
heavy chain kinase
Not Identified
42
ABC1 family protein kinase, ABC1-A
subfamily protein kinase
ABC1 kinase domain; yeast ABC1
essential for electron transfer in the
BC(1) complex; E.coli homolog
required for ubiquinone biosynthesis
ABC1 family protein kinase, ABC1-C
subfamily protein kinase
putative actin fragmin kinase
putative AFK family protein kinase,
putative actin fragmin kinase
putative actin fragmin kinase
DPU_G0068144
90360
DDB_G0279609
DDB_G0279609
AFK family protein kinase, actin
fragmin kinase, protein kinase,
Atypical group
DPU_G0060816
75494
DDB_G0270170
DDB_G0270170
DPU_G0061336
98971
DDB_G0293800
DDB_G0293800
BRD family protein kinase, GTE group
protein, bromodomain-containing
protein
BRD family protein kinase, BTB/POZ
domain-containing protein, GTE group
protein, ankyrin repeat-containing
protein
DPU_G0073684
150585
DDB_G0279761
DDB_G0279761
G11 family protein kinase, protein
kinase, Atypical group, putative
protein serine/threonine kinase
DPU_G0052622
33395
rio1
DDB_G0280431
rio1
DPU_G0063456
156778
rio2
DDB_G0282099
rio2
RIO family protein kinase, RIO1
subfamily protein kinase, protein
kinase, Atypical group, putative
protein serine/threonine kinase
RIO family protein kinase, RIO2
subfamily protein kinase, protein
kinase, Atypical group, putative
protein serine/threonine kinase
DPU_G0059476
49312
torA
DDB_G0281569
tor
DPU_G0073170
150412
atr1
DDB_G0291380
atr1
DPU_G0064214
157099
smg1
DDB_G0275845
smg1
DPU_G0073432
150499
dnapkcs
DDB_G0281167
dnapkcs
DPU_G0074948
151088
tra1
DDB_G0281947
tra1
DPU_G0059428
98741
taf1
DDB_G0292242
taf1
DPU_G0074374
93469
tif1
DDB_G0271372
DDB_G0271372
FRAP subfamily protein kinase, PIKK
family protein kinase,
phosphatidylinositol 3-kinase-related
protein kinase
ATR subfamily protein kinase, PIKK
family protein kinase,
phosphatidylinositol 3-kinase-related
protein kinase
PIKK family protein kinase, SMG1
subfamily protein kinase,
phosphatidylinositol 3-kinase-related
protein kinase
DNA-dependent protein kinase
(DNAPK) subunit, PIKK family
protein kinase, phosphatidylinositol 3kinase-related protein kinase
PIKK family protein kinase, TRRAP
subfamily protein kinase,
phosphatidylinositol 3-kinase-related
protein kinase
HAF group protein, TAF1 family
protein kinase, TFIID subunit,
bromodomain-containing protein
TIF1 family protein kinase, B-box zinc
finger-containing protein, Kelch
repeat-containing protein, RING zinc
finger-containing protein.
Grey bars indicate major divisions in protein kinase groups (ePK, unclassified, atypical) and colored
blocks roughly divide the predicted genes into protein kinase subfamilies.
43
G-protein coupled receptors (or seven transmembrane domain receptors)
G-protein coupled receptors (GPCRs) are subdivided into six major families that, aside from
their conserved secondary domain structure, do not share significant sequence similarity across
families [121]. Family 1 includes the -adrenergic, light and odorant receptors, family 2
receptors are activated by large peptides like glucagon or secretin, family 3 comprises the
metabotropic glutamate receptors, Ca2+-sensing receptors, a group of putative pheromone
receptors coupled to G0 and the GABAB receptors, family 4 contains pheromone receptors
associated with Gi, family 5 includes the frizzled and smoothened receptors involved in
embryonic development and family 6 the Dictyostelium cAMP receptors [121]. Table S10 lists
all D. purpureum and D. discoideum members of the six major GPCR families.
Family 1 includes the -adrenergic, light and odorant receptors; the family 2 receptors are
activated by large peptides like glucagon or secretin; the family 3 receptors include the
metabotropic glutamate receptors, Ca2+-sensing receptors, a group of putative pheromone
receptors coupled to G0, and the GABAB receptors; and the family 4 receptors include
pheromone receptors associated with Gi; the family 5 receptors include the frizzled and
smoothened receptors involved in embryonic development; and the family 6 receptors include
the cAMP receptors of the social amoeba [121].
The original analysis of the D. discoideum genome revealed 55 genes predicted to encode
GPCRs; eight cAMP receptors (cAR) and cAMP receptor-like (crl) proteins, one secretin-like
receptor (family 2), 17 GABAB-like receptors (family 3), and 25 frizzled-like receptors (family
5)[1, 122]. The analysis of a group 1 and group 2 dictyostelid genome (Dictyostelium
fasciculatum and Polysphondylium pallidum, respectively) resulted in the identification of seven
44
additional putative GPCR genes in D. discoideum genome, bringing the number to 62. These
belong to two subgroups of orphan receptors. Six putative GPCRs, of which one appears
incorrectly predicted because it lacks two transmembrane domains, are related to vertebrate
transmembrane protein 145. The seventh putative receptor is highly conserved from amoeba to
man and belongs to the GPR89 group of receptors. There are two such receptors in Arabidopsis
thaliana, GTG1 and GTG2 (GPCR-type G protein 1 and 2) and recently it was reported that they
constitute abscisic acid receptors [123].
Most of the receptors in both species were already present in the common ancestor, while
some, such as carB, appear to have expanded only in D. discoideum, or else duplicated versions
were lost in D. purpureum. Other GPCR’s such as grlK and grlM appear to have been duplicated
from an ancestral gene in both organisms. The data suggest an evolutionary trend in the
Dictyostelids towards a higher number and larger diversity of GPCRs. Interestingly, our analysis
revealed three exceptions to this observation; there is exactly one ortholog for the GPR89 gene,
an ortholog for each D. discoideum crl gene, and the D. purpureum genome encodes two
latrophilin-like (family 2) receptors, while D. discoideum has one full length latrophilin and a
second smaller predicted protein that may or may not be functional. Before their description in
the Dictyostelids family 2 receptors were thought to be of relatively recent origin, appearing
closer to the time of the divergence of animals [124].
45
Figure S11. The repertoire of D. purpureum and D. discoideum G-protein coupled
receptors. A CLUSTALX alignment of the sequences encompassing the seven transmembrane domains
of all D. purpureum and D. discoideum GPCRs, as well as selected GPCRs from other organisms, was
used to create a dendrogram with the TreeView program. A black circle marks the innermost node of each
46
branch supported by >50% bootstraps. Protein Ids (Dp) were used for the D. purpureum, dictyBase
identifiers (DDB) for the D. discoideum, gene names for the Polysphondylium pallidum and SwissProt
entry names for all other receptors. F1: Family 1; F2: Family 2; CAR/CRL: cAMP receptor/cAMP
receptor-like. ARATH: Arabidopsis thaliana, POLPA: P. pallidum, CAEEL: Caenorhabditis elegans,
DROME: Drosophila melanogaster; BOVIN: Bos taurus; GEOCY: Geodia cydonium; HUMAN: Homo
sapiens.
Table S10. The G-protein coupled receptors of D. purpureum and D. discoideum.
D. discoideum
dictyBase
Gene I.D.
D. purpureum
Protein
Name
dictyBase
Gene I.D.
Protein
ID
DDB_G0273397 CAR1/carA*
cAR1
DPU_G0064058
99295
carA
cAR1
KPGIBL
DDB_G0288179 CAR2/carB
DDB_G0277829 CAR3/carC
DDB_G0277831 CAR4/carD
cAR2
cAR3
cAR4
DPU_G0053090
-----
92050
-----
carB
-----
cAR2
-----
BKPGIBL
-----
crlA
CrlA
DPU_G0054582
34601
crlA
CrlA
BKPGIBL
crlB
crlC
crlD
crlE
crlF
crlG
CrlB
CrlC
CrlD
CrlE
CrlF
CrlG
DPU_G0060408 155536
DPU_G0068592 158756
DPU_G0063516 75785
DPU_G0061572 82126
DPU_G0054366 94711
DPU_G0066748 58375
crlB
crlC
crlD
crlE
crlF
crlG
CrlB
CrlC
CrlD
CrlE
CrlF
CrlG
BBL
BGIBL
IBL
BIBL
GIBL
BGIBL
Serpentine
DDB_G0283615
receptor
PIP5K family
rpkA
RpkA DPU_G0064944
99415
rpkA
RpkA
BGIBL
Latrophilin
DDB_G0286037
receptor-like
(Family 2):
lrlA
LrlA
DPU_G0074886 151051
lrlA1
LrlA1
KPGIBL
DDB_G0286109
GABA(B) or DDB_G0271684
metabotropic
glutamate
receptor-like
(Family 3):
DDB_G0271686
DDB_G0282461
DDB_G0286895
DDB_G0291356
DDB_G0282175
DDB_G0272244
DDB_G0282459
DDB_G0272150
DDB_G0269386
DDB_G0281211
DDB_G0286643
--grlA
--GrlA
DPU_G0057912
--DPU_G0052600
95036
--33314
lrlA2
--grlA
LrlA2
--GrlA
KPGIBL
--BKPGIBL
grlB
grlC
grlD
grlE
grlF
grlG
grlH
grlJ
grlK
grlL
grlM
GrlB
GrlC
GrlD
GrlE
GrlF
GrlG
GrlH
GrlJ
GrlK
GrlL
GrlM
DPU_G0053524 152547
--------DPU_G0051870 151807
----DPU_G0070356 159361
----DPU_G0052598 78826
DPU_G0055180 15906
DPU_G0053314 16140
DPU_G0055176 34997
grlB
----grlE
--grlG
--grlJ
grlK
grlL
grlM
GrlB
----GrlE
--GrlG
--GrlJ
GrlK
GrlL
GrlM
KPGIBL
----BKPGIBL
--BKPGIBL
--KPGIBL
KPGIBL**
BKPGIBL
BKPGIBL**
cAMP
Receptors:
cAMP
DDB_G0280983
Receptor-like:
DDB_G0289395
DDB_G0283619
DDB_G0283579
DDB_G0286301
DDB_G0290185
DDB_G0279599
Gene Name(s)
47
Proposed
Proposed
Evidence*
Gene Name Protein Name
DDB_G0283839
DDB_G0271688
DDB_G0291095
DDB_G0287905
DDB_G0287681
Frizzled/Smo
othened-like
or FSL
(Family 5):
fsl Group
DDB_G0284761
(Frizzled/Smo
othened-Like)
DDB_G0270730
DDB_G0274287
DDB_G0269528
DDB_G0288269
DDB_G0288253
DDB_G0288261
DDB_G0274773
DDB_G0272885
DDB_G0284729
DDB_G0284585
DDB_G0273035
DDB_G0270672
DDB_G0278289
DDB_G0286607
DDB_G0286609
fsc Group
DDB_G0289725
(Frizzled/Smo
othened-like
Sans CRD)
DDB_G0282989
DDB_G0292204
DDB_G0272240
DDB_G0272306
DDB_G0292064
DDB_G0292156
DDB_G0292100
DDB_G0292102
grlN
grlO
grlP
grlQ
grlR
GrlN
GrlO
GrlP
GrlQ
GrlR
----DPU_G0061448
DPU_G0059522
DPU_G0059524
----98995
81373
98759
----grlP
grlQ
grlR
----GrlP
GrlQ
GrlR
----BPGIBL
BKGIBL
BGIBL
fslA
FslA
DPU_G0070308 159333
fslA
FslA
BGIBL
fslB
fslC
fslD
fslE
fslF
fslG
fslH
fslJ
fslK
fslL
fslM
fslN
fslO
fslP
fslQ
fscA
FslB
FslC
FslD
FslE
FslF
FslG
FslH
FslJ
FslK
FslL
FslM
FslN
FslO
FslP
FslQ
FscA
DPU_G0057226 56349
--------------------DPU_G0067680 17639
DPU_G0071614 85139
DPU_G0055030 153271
DPU_G0064402 89818
----DPU_G0059206 155058
----DPU_G0066984 41820
DPU_G0061414 82049
DPU_G0055116 79778
fslB
----------fslH
fslJ
fslK
fslL
--fslN
--fslP
fslQ
fscA
FslB
----------FslH
FslJ
FslK
FslL
--FslN
--FslP
FslQ
FscA
BKGIBL
----------BGIBL
GIBL
BGIBL
BGIBL
--BBL
--BBL
BL
BBL
fscB
fscC
FscB
FscC
--DPU_G0064888
--99405
--fscC1
--FscC1
--BGIBL
fscD
fscE
fscF
fscG
fscH
fscJ
FscD
FscE
FscF
FscG
FscH
FscJ
DPU_G0055752 18554
--------DPU_G0052082 26238
----DPU_G0052084 147382
DPU_G0052086 74651
fscC2
----fscF
--fscH
fscJ
FscC2
----FscF
--FscH
FscJ
GIBL
----BKGIBL
--BBL
BBL
*B: Best Bidirectional BLAST Hit; K: KOG; P: Pfam; G: GO; I: InterPro; BL: manual BLAST
** 15906 is likely the orthologue of GrlK (based on BBB 34997 is the orthologue of GrlM; see also the
phylogenetic tree)
48
Transcription Factors
The overall comparison of the recognizable transcription factors in D. discoideum and D.
purpureum shows gross conservation both in terms of the total number of genes in each of the
transcription factor families and also at the protein sequence level for each predicted protein.
Table S11. The Transcription factors of D. purpureum – Summary.
TF family
Zinc finger GATA
STAT
Helix-turn-helix
bZIP
MADS box
Myb
bHLH
CBF/NF-Y
SNF5
E2F/DP
WRKY
Zinc-Cluster TF
Fork Head activators
Other unique TFs
Total number in
D. purpureum
16
4
12
11
2
32
0
3
3
1
2
1
4
5
Total number in
D. discoideum
25
4
15
19
4
36
0
2
3
1
1
2
2
4
Transcription Factor Families (detail).
D. purpureum
Protein I.D.
BZIP Family
91709
152822
96504
149168
150254
92949
41441
156583
N.D.
93022
N.D.
96995
N.D.
N.D.
N.D.
N.D.
98369
N.D.
N.D.
150629
155482
42334
D. purpureum
dictyBase
Gene I.D.
Predicted D.
discoideum
ortholog
D. discoideum
dictyBase
Gene I.D.
Annotation
DPU_G0073166
DPU_G0054020
DPU_G0054134
DPU_G0067176
DPU_G0072470
DPU_G0065610
DPU_G0066112
DPU_G0063022
BzpB
BzpA/DimA
BzpC
BzpD
BzpE
BzpF
BzpG
BzpH
BzpI
BzpJ
BzpK
BzpL
BzpM
BzpN
BzpO
BzpP
BzpQ
BzpR
BzpS
No bZIP domain
No bZIP domain
No bZIP domain
DDB_G0291372
DDB_G0278971
DDB_G0279439
DDB_G0278379
DDB_G0269338
DDB_G0279529
DDB_G0282749
DDB_G0277681
DDB_G0290173
DDB_G0274993
DDB_G0282049
DDB_G0284023
DDB_G0282047
DDB_G0286411
DDB_G0290169
DDB_G0290303
DDB_G0288705
DDB_G0290165
DDB_G0290171
DIF-signaling
DIF-signaling
DPU_G0066952
DPU_G0067218
DPU_G0056250
DPU_G0073814
DPU_G0060208
DPU_G0068042
49
CREB candidate
CREB candidate
GCN4 homolgue
mafK
mRNA capping enzyme
STAT Family
57361
157342
147158
51917
MADS Box
Family
92150
N.D.
N.D.
96067
GATA Family
N.D.
51958
N.D.
96381
90623
96721
55210
55210
97535
99939
77444
82915
99939
155826
159043
151306
N.D.
N.D.
N.D.
83500
N.D.
83500
83500 (49.7)
N.D.
91945
92966
72172
81331
150926
77360
82915
Myb Family
26731
94790
44316
(99144)
99144
(99144)
51636
150027
98959
152142
159839
75617
92812
59013
DPU_G0061618
DPU_G0064844
DPU_G0074350
DPU_G0073854
DstA
DstD
DstC
DstB
DDB_G0281381
DDB_G0275167
DDB_G0268638
DDB_G0293532
DPU_G0054446
SrfA
SrfB
SrfC
SrfD
DDB_G0281387
DDB_G0282835
DDB_G0268920
DDB_G0283483
StkA
ComH
GtaC
GtaD
GtaE
GtaF
GtaG
GtaH
GtaI
GtaJ
GtaK
GtaL
GtaM
GtaN
GtaO
GtaP
GtaQ
GtaR
GtaS
GtaT
GtaU
GtaV
GtaW
GtaX
GtaY
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
N.D.
DDB_G0277147
DDB_G0280547
DDB_G0277589
DDB_G0286855
DDB_G0267640
DDB_G0268792
DDB_G0270756
DDB_G0277591
DDB_G0281661
DDB_G0281829
DDB_G0282811
DDB_G0285139
DDB_G0286837
DDB_G0287057
DDB_G0289651
DDB_G0295707
DDB_G0286843
DDB_G0279331
DDB_G0280627
DDB_G0280639
DDB_G0280853
DDB_G0281087
DDB_G0286839
DDB_G0290665
DDB_G0279239
MybA
MybB
MybC
MybD
MybE
MybF
MybG
MybH
MybI
MybJ
MybK
MybL
MybM
MybN
DDB_G0293900
DDB_G0275445
DDB_G0281563
DDB_G0287637
DDB_G0281969
DDB_G0278317
DDB_G0288783
DDB_G0277927
DDB_G0289151
DDB_G0274463
DDB_G0276877
DDB_G0285373
DDB_G0267636
DDB_G0292782
DPU_G0070868
DPU_G0074602
DPU_G0074318
DPU_G0070286
DPU_G0060732
DPU_G0052890
DPU_G0052890
DPU_G0074600
DPU_G0070362
DPU_G0073586
DPU_G0064036
DPU_G0070362
DPU_G0061040
DPU_G0069464
DPU_G0075458
DPU_G0065622
DPU_G0065622
DPU_G0065622
DPU_G0051784
DPU_G0065836
DPU_G0074742
DPU_G0059436
DPU_G0074694
DPU_G0073296
DPU_G0064036
Myb Family
DPU_G0055346
DPU_G0055088
DPU_G0073496
DPU_G0062828
DPU_G0062828
DPU_G0062828
DPU_G0071282
DPU_G0071646
DPU_G0061114
DPU_G0052522
DPU_G0071950
DPU_G0061760
DPU_G0063666
DPU_G0070466
50
96894
76145
93079
N.D.
79414
N.D.
99744
99058
156055
152374
97062
N.D.
38843
76451
77715
29919
159517
26655
156868
148146
149794
85378
150076
4822
26731
11392
75617
155440
154597
77715
55593
151821
Homeobox
Family
96898
96404
159280
149222
N.D.
14027
91524
N.D.
92118?
24166
39700
160463
91760
154980
91524
D. purpureum
Protein I.D.
Other Families
13314
N.D.
159469
DPU_G0064680
DPU_G0066540
DPU_G0067830
MybO
MybP
MybQ
MybR
MybS
MybT
MybU
MybV
MybW
MybX
MybY
MybZ
MybAA
bdp1
cdc5l
DDB_G0278179
DDB_G0288747
DDB_G0271272
DDB_G0280079
DDB_G0286135
DDB_G0277033
DDB_G0267638
DDB_G0280705
Isw
DDB_G0290787
DDB_G0270560
DDB_G0289319
DDB_G0292182
DDB_G0293468
DDB_G0292180
DDB_G0283953
DDB_G0279281
DDB_G0270346
DDB_G0288285
DDB_G0284399
DDB_G0284103
DDB_G0268368
DDB_G0283405
DDB_G0279311
DDB_G0278179
DDB_G0288747
DDB_G0271272
DDB_G0280079
DDB_G0286135
DDB_G0277033
DDB_G0267638
DDB_G0280705
DDB_G0292948
WarA
Hbx2
DDB_G0284293
DDB_G0286733
DDB_G0289677
DDB_G0291197
DDB_G0273127
DDB_G0277505
DDB_G0278225
DDB_G0272967
DDB_G0280473
DDB_G0279257
DDB_G0288975
DDB_G0295787
DDB_G0273645
DDB_G0291075
DDB_G0275173
DDB_G0284293
DDB_G0286733
DDB_G0289677
DDB_G0291197
DDB_G0273127
DDB_G0277505
DDB_G0278225
DDB_G0272967
DDB_G0280473
DDB_G0279257
DDB_G0288975
DDB_G0295787
DDB_G0273645
D. purpureum
dictyBase Gene I.D.
Predicted D.
discoideum
ortholog
D. discoideum
dictyBase Gene I.D.
DPU_G0063568
DDB_G0279419
DDB_G0282697
N.D.
DDB_G0279419
DDB_G0282697
DPU_G0054254
DPU_G0068302
DPU_G0061846
DPU_G0061568
DPU_G0053088
DPU_G0068490
DPU_G0061406
DPU_G0068518
DPU_G0074540
DPU_G0070078
DPU_G0070840
DPU_G0054730
DPU_G0063714
DPU_G0059390
DPU_G0070570
DPU_G0072576
DPU_G0071826
DPU_G0071212
DPU_G0055346
DPU_G0073554
DPU_G0061760
DPU_G0060138
DPU_G0058108
DPU_G0074540
DPU_G0054422
DPU_G0051898
DPU_G0064692
DPU_G0074442
DPU_G0070146
DPU_G0067434
DPU_G0061474
DPU_G0068748
DPU_G0054012
DPU_G0053458
DPU_G0062888
DPU_G0074296
DPU_G0073884
DPU_G0059052
DPU_G0068748
DPU_G0070684
51
only myb domain
human CDC5L
Annotation
putative CCAAT-binding
transcription factor
putative histone-like
92261
DPU_G0055668
N.D.
158603
158872
DPU_G0068148
DPU_G0068892
cbfA
cbfB
DDB_G0279409
DDB_G0293470
98517
DPU_G0057322
E2F
DDB_G0284129
86591
13896
157864
94676
DPU_G0066084
DPU_G0066086
DPU_G0066170
DPU_G0053996
wrky1
N.D.
crtF
DDB_G0275267
99541
151803
N.D.
55079
157374
49599
97029
N.D.
84008
100178
DPU_G0066152
DPU_G0051862
gbfA
DDB_G0291348
DDB_G0270590
DDB_G0290591
tipA
N.D.
N.D.
DDB_G0277305
DDB_G0279373
DDB_G0284591
DDB_G0288755
DDB_G0291348
DDB_G0270590
DDB_G0290591
DDB_G0281561
DPU_G0052332
DPU_G0064900
DPU_G0060490
DPU_G0067962
DPU_G0067382
DPU_G0074078
DDB_G0278077
DDB_G0277305
DDB_G0279373
DDB_G0284591
transcription factor
N-terminus is similar to
CCAAT-box binding
transcription factor
C-module-binding factor
transcription factor jumonji,
jmjC domain-containing
protein
transcription factor
E2F/dimerisation partner
(TDP) family protein
putative WRKY
transcription factor
CAR1 Transcription Factor
required for expression of
aggregation genes
zinc cluster transcription
factor
winged helix DNA-binding
domain-containing protein
Fork head activators
SNF5/SMARCB1/INI1
family protein, chromatin
remodeling complex
subunit E (CHE) protein;
SNF5 homolog
N.D. No ortholog detected.
The microfilament system
In D. purpureum 31 actin and actin-related genes and two putative pseudogenes have been
identified (Table S12; Figure S12). This contrasts with the 41 genes and 7 pseudogenes of the D.
discoideum actinome [125]. The D. purpureum actinome encodes 10 different proteins (versus
17 in D. discoideum). There is a large group of genes (12) encoding an identical protein in turn
identical to D. discoideum actin 10. In D. discoideum a group of 17 genes encodes an identical
product, actin 8. A smaller group of 3 genes of D. purpureum encodes an identical actin (Actin
S) that differs in only one residue from actin 10 (M190L) and in two residues from actin 8 (D2E,
M190L). Of the two pseudogenes one appears to be an act10 gene with a frame shift caused by
two missing bases and the other is a truncated gene with additional missing bases in the coding
52
region. One gene (fia) encodes a filactin ortholog and 7 genes encode fairly divergent actins
without direct orthologs in the D. discoideum actinome (Figure S12). Almost all D. purpureum
actin genes have a single conserved intron position, whereas D. discoideum genes are intronless,
indicating that all conventional D. purpureum actin genes resulted from the duplication of a
single ancestral gene. D. purpureum has the same set of actin related proteins (Arp’s) as D.
discoideum, although with variable degree of amino acid sequence similarity (98% for Arp1,
versus 58% for Arp8). Among the proteins involved in nucleation of actin filaments, D.
purpureum has an additional formin gene, forK. The C-terminal part of ForK is closer to ForA
than to any other formin but lacks the DAD (diaphanous autoinhibitory domain) region. Since
the forK gene is intronless and the forA gene has 4 introns, we speculate that forK resulted from
the integration and subsequent divergence of a retrotranscribed forA gene.
D. purpureum has a single gene encoding the G-actin sequestering protein actobindin. In
D. discoideum the family is represented by a tandem of three genes, two encoding the same
protein. D. purpureum actobindin is equally similar to both D. discoideum actobindins. There are
also some differences in the set of profilins. D. purpureum has 4 profilin genes, compared to the
3 of D. discoideum. Two of them, proA and proC, have direct orthologs in D. discoideum. There
is no proB, which is probably the result of a duplication of an ancestral proC in D. discoideum
only, but the unique D. purpureum genes proD and proE share two intron positions with proA,
suggesting that they arose by duplications of this gene in D. purpureum.
The ADF/cofilin family also differs between both Dictyostelium species. A phylogenetic
tree of all ADF domains encoded by the genomes of both species allows distinguishing three
major groups (Figure S13).
53
Hisactophilin is represented by a single protein in D. purpureum that is related to the D.
discoideum hisactophilins A and B. Both annexin genes of D. discoideum are represented in D.
purpureum. Additionally, one more gene in D. purpureum, nxnC, appears to encode a truncated
protein identical to the C-terminus of annexin I. Among the translation elongation factors with
actin-binding properties, D. purpureum has one single gene encoding an EF1a (two in D.
discoideum) and two genes encoding EF1b and related proteins (three in D. discoideum).
D. purpureum contains 10 genes (and two pseudogenes) that are weakly similar to the
group of 16 D.discoideum ponticulins (ponA, DDB_G0293522; ponB, DDB_G0286247; ponC1,
DDB_G0286717; ponC2, DDB_G0286715; ponC3, DDB_G0286721; ponC4, DDB_G0286719;
ponC5, DDB_G0286723; ponD, DDB_G0282423; ponE, DDB_G0293634; ponF,
DDB_G0286631; ponG/pspA, DDB_G0267412; ponH, DDB_G0286573; ponJ,
DDB_G0289919; ponK, DDB_G0268460; ponL, DDB_G0288649; ponM, DDB_G028198).
Apart from 4 D. purpureum ponticulins and 5 D. discoideum ponC isoforms that constitute two
separate clusters of very similar proteins, in general all ponticulins are equally distant, and direct
orthologs between both species cannot be identified. One D. purpureum ponticulin (92055)
consists of an internal duplication of the central region, and therefore contains two blocks of 6
cysteines.
Table S12. The microfiliament system of D. purpureum.
D. purpurem D. purpureum
Protein ID dictyBase Gene
I.D.
Actins
73394
DPU_G0065618
92832
DPU_G0063988
73240
DPU_G0063614
92793
DPU_G0063284
72679
DPU_G0056118
92254
DPU_G0055648
54009
DPU_G0071500
Proposed
gene name
Proposed D.
purpureum
protein name
D. discoideum
ortholog
D. discoideum
gene ID
Relevant domains
act10
act10
act10
act10
act10
act10
act10
Actin 10
Actin 10
Actin 10
Actin 10
Actin 10
Actin 10
Actin 10
act10
act10
act10
act10
act10
act10
act10
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
Actin
Actin
Actin
Actin
Actin
Actin
Actin
54
46519
91566
91392
91170
91068
90232
DPU_G0071452
DPU_G0069822
DPU_G0063498
DPU_G0053430
DPU_G0069316
DPU_G0067308
92405
DPU_G0057900
act10
act10
act10
act10
act10
pseudogene
(act10)
actS
48914
DPU_G0057898
actS
72359
DPU_G0052194
actS
80660
DPU_G0057356
fia
74418
DPU_G0073124
actT
74419
DPU_G0073126
actU
87084
DPU_G0072460
actV
74427
DPU_G0073142
actW
78745
DPU_G0052426
actX
88965
DPU_G0059126
actY
95143
DPU_G0059050
actZ
74420
DPU_G0073128 pseudogene
Actin-related proteins
88548
DPU_G0056364
arpA
46175
DPU_G0068768
arpB
50380
DPU_G0064164
arpC
48789
DPU_G0056898
arpD
154327
DPU_G0057282
arpE
99023
DPU_G0061582
arpF
158218
DPU_G0067228
arpG
155548
arpH
DPU_G0060434
Actin 10
Actin 10
Actin 10
Actin 10
Actin 10
act10
act10
act10
act10
act10
act10/act8
act10/act8
act10/act8
none
fia
none
none
none
none
none
none
none
Filactin
Arp1
Arp2
Arp3
Arp4
Arp5
Arp6
Arp8
Arp11
Nucleators and WH2 domain-containing proteins
150581
DPU_G0073676
forA
Formin A
33735
DPU_G0053232
forB
Formin B
50865
DPU_G0066776
forC
Formin C
46912
DPU_G0073848
forD
Formin D
154316
DPU_G0057262
forE
Formin E
148204
DPU_G0059834
forF
Formin F
153797
DPU_G0056158
forG
Formin G
156963
DPU_G0063964
forH
Formin H
36102
DPU_G0056740
forI
Formin I
97202
DPU_G0070450
forJ
Formin J
99159
DPU_G0062882
forK
Formin K
94694
DPU_G0054232
abn
Actobindin
156917 and DPU_G0063804
40920
and
DPU_G0065084
87126
DPU_G0072896
81492
DPU_G0059876
(no model)
74538
DPU_G0075208
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811
DDB_G0289811,
DDB_G0269234
DDB_G0289811,
DDB_G0269234
DDB_G0289811,
DDB_G0269234
DDB_G0284389
Actin
Actin
Actin
Actin, FLMN
Actin
Actin
Actin
Actin
Actin
Actin
Actin
Actin
arpA
arpB
arpC
arpD
arpE
arpF
arpG
arpH
DDB_G0288937
DDB_G0272106
DDB_G0283755
DDB_G0280887
DDB_G0291728
DDB_G0287007
DDB_G0287779
DDB_G0287739
Actin
Actin
Actin
Actin
Actin
Actin
Actin
Actin
forA
forB
forC
forD
forE
forF
forG
forH
forI
forJ
none
abnA and abnB/abnC
DDB_G0279607
DDB_G0282297
DDB_G0287295
DDB_G0282245
DDB_G0269626
DDB_G0289763
DDB_G0277175
DDB_G0285589
DDB_G0284519
DDB_G0291378
FH2
FH2
FH2
FH2
FH2
FH2
FH2
FH2
FH2
FH2
FH2
WH2
scrA
Scar
scrA
DDB_G0270884,
DDB_G0269518,
DDB_G0269520
DDB_G0285253
wasA
WASP
WASP-related 1
WASP-related 2
Scar/WASPrelated
wasA
DDB_G0272811
DDB_G0283827
DDB_G0292878
DDB_G0293834
DDB_G0272811
DDB_G0283827
DDB_G0292878
55
Actin
Actin
Actin
Actin
Actin
Actin
WH2
WH2
WH2
WH2
WH2
76111
150808
DPU_G0066048
DPU_G0074280
153613
DPU_G0055738
79620
DPU_G0054788
wipA
WIPa
WH2 and SH3
containing
WH2 and LIM
containing
WH2 and FYVE
containing prot.
kinase
WH2 domaincontaining
VASP
CARMIL
PIR121 (Scar
complex)
Nap1 (Scar
complex)
Abi2 (Scar
complex)
HSPC300 (Scar
complex)
ARPC1/p41-Arc
(Arp2/3
complex)
ARPC2/p34-Arc
(Arp2/3
complex)
ARPC3/p21-Arc
(Arp2/3
complex)
ARPC4/p20-Arc
(Arp2/3
complex)
ARPC5/p16-Arc
(Arp2/3
complex)
wipA
DDB_G0269708
DDB_G0270430
DDB_G0269708
WH2
WH2
limD
DDB_G0291251
WH2, LIM
slob1
DDB_G0281863
WH2
DDB_G0281723
DDB_G0281723
WH2
vasP
carmil
pirA
DDB_G0289541
DDB_G0292386
DDB_G0287855
napA
DDB_G0274519
abiA
DDB_G0267956
hspc300
DDB_G0279175
arcA
DDB_G0277825
arcB
DDB_G0282813
acrC
DDB_G0292804
arcD
DDB_G0269102
arcE
DDB_G0288319
proA
proC
proD
proE
Profilin 1
Profilin 3
Profilin 4
Profilin 5
proA
proC
none
none
DDB_G0287125
DDB_G0271142
PRO
PRO
PRO
PRO
cofA
Cofilin 1
cofA (and cofB)
DDB_G0277833
(DDB_G0291970)
ADF
Cofilin-related
none
Glia maturation
gmfA
DDB_G0282595
factor
Twinfilin
twfA
DDB_G0274437
Coactosin
coaA
DDB_G0293898
Abp1
abpE
DDB_G0273447
CoactosinDDB_G0283837
DDB_G0283837
related
CoactosinDDB_G0273569_ps, DDB_G0273569,
related
DDBG_0273405_ps DDBG_0273405
CoactosinDDB_G0277615
DDB_G0277615
related
CoactosinDDB_G0295683
DDB_G0295683
related LIMcontaining
ADF
ADF
slob1
(no model)
91862
98559
46589
DPU_G0075368
DPU_G0057980
DPU_G0071848
vasP
carmil
pirA
153775
DPU_G0056120
napA
87985
DPU_G0053536
abiA
88267
DPU_G0054936
hspc300
95056
DPU_G0058120
arcA
159207
DPU_G0069920
arcB
58101
DPU_G0065124
acrC
85721
DPU_G0062552
arcD
59079
DPU_G0070712
arcE
Profilins
91884
DPU_G0075524
90584
DPU_G0069940
157060
DPU_G0064146
157061
DPU_G0064148
Cofilin family
57070
DPU_G0060220
155430
88870
DPU_G0060116
DPU_G0058504
cofG
gmfA
44803
45162
84230
84356
DPU_G0073040
DPU_G0055352
DPU_G0068122
DPU_G0068594
twfA
coaA
abpE
88560
DPU_G0056402
91304
DPU_G0059796
41497
DPU_G0066212
56
ADF
ADF
ADF
ADF
ADF
ADF
ADF
48521
DPU_G0055848
148253
DPU_G0060306
57957
DPU_G0064410
Gelsolin family
46298
DPU_G0069786
153835
DPU_G0056220
(no model)
51061
DPU_G0067882
Coactosinrelated
Coactosinrelated
Coactosinrelated
vilA
vilB
vilC
vilD
Villidin
Protovillin
DDB_G0290593
DDB_G0290593
ADF
DDB_G0270134,
DDB_G0270132
none
DDB_G0270134,
DDB_G0270132
ADF
vilA
vilB
vilC
vilD
DDB_G0288557
DDB_G0276453
DDB_G0271058
DDB_G0282725
WD, GEL, VHP
GEL, VHP
GEL, VHP
GEL, VHP
sevA
gnrA
gnrB
gnrC
DDB_G0289327
DDB_G0291125
DDB_G0291536
DDB_G0276571
GEL
GEL
GEL
GEL
WD
WD
ADF
99974
4927
95982
90830
Varia
82038
99654
53913
45371
97675
51240
94447
92199
38686
75958
96363
DPU_G0070708
DPU_G0067876
DPU_G0069738
DPU_G0071952
sevA
gnrA
gnrB
gnrC
Flightless/villinrelated
Severin
GRP125
Gelsolin-related
Gelsolin-related
DPU_G0067358
DPU_G0070758
DPU_G0058872
DPU_G0075686
DPU_G0068950
DPU_G0051748
DPU_G0054986
DPU_G0061038
DPU_G0064986
DPU_G0073056
corA
corB
cap
acpA
acpB
wdpA
abpB
dct
comA
cmr
hat
Coronin
Coronin 7
CAP
Cap32
Cap34
Aip
ABP34
Dynacortin
Comitin
Comitin-related
Hisactophilin
corA
corB
cap
acpA
acpB
wdpA
abpB
dct
comA
cmr
hatA and hatB
97523
DPU_G0074506
nxnA
nxnA
12667
83254
153006
DPU_G0074620
DPU_G0064926
DPU_G0054464
nxnB
nxnC
nxnB
nxnB
DDB_G0281499
DDB_G0284261
DDB_G0284261
DDB_G0281499
49816
DPU_G0061526
DDB_G0285939
DDB_G0285939
52946
DPU_G0060246
efaAI
efaAI
DDB_G0269134
149388
DPU_G0068476
efa1B
efa1B
DDB_G0284035
93663
DPU_G0059322
DDB_G0286023
DDB_G0286023
94172
87008
152393
79698
54776 and
91894
91686
32515
94684
99774
DPU_G0073190
DPU_G0071698
DPU_G0053124
DPU_G0054948
54776 and 91894
mhkA
Annexin VII
(C1)
Annexin I
Annexin I
Vinculin/alphacatenin-related
Vinculin/alphacatenin-related
Elongation
factor IA
Elongation
factor IB
Elongation
factor IB-related
MHCKA
DDB_G0267382
DDB_G0269388
DDB_G0288769
DDB_G0267374
DDB_G0272104
DDB_G0278733
DDB_G0279081
DDB_G0283767
DDB_G0289599
DDB_G0279711
DDB_G0282141,
DDB_G0282143
DDB_G0269160
mhkA
DDB_G0278025
DDB_G0288031
DDB_G0279449
DDB_G0279093
DDB_G0291231
DDB_G0278025
DDB_G0288031
DDB_G0279449
DDB_G0279093
VHP
VHP
VHP
KELCH
DPU_G0072514
DPU_G0051412
DPU_G0054034
DPU_G0068600
limC
limD1
limE
limC
limD1
limE
DDB_G0283983
DDB_G0277881
DDB_G0287507
DDB_G0279415
DDB_G0283983
LIM
LIM
LIM
FLMN
Kelch-related
LimC
LimD1
LimE
Filamin and
HECT
containing
57
WD
50592
DPU_G0065142
LRR and filamin
repeat
containing
91016
DPU_G0057526
Ponticulin
92054
DPU_G0053170
Ponticulin
159218
DPU_G0069944
Ponticulin
97951
DPU_G0053176
Ponticulin
152487
DPU_G0053306
Ponticulin
152347
DPU_G0053044
Ponticulin
153835
DPU_G0056220
Ponticulin
76224
DPU_G0067146
Ponticulin
155499
DPU_G0060344 pseudogene
Ponticulin
80458
DPU_G0056822 pseudogene
Ponticulin
148939
DPU_G0065406
Ponticulin
92055
DPU_G0053172
Ponticulin
I/LWEQ domain containing proteins
48677
DPU_G0056558
hipA
Sla2/HIP-1
50735
DPU_G0065934
talA
Talin A
(Filopodin)
148964
DPU_G0065666
talB
Talin B
81926
DPU_G0061044
85023
DPU_G0071020
158187
DPU_G0067092
Myosins
48616
DPU_G0056248
mhcA
Myosin II
157695
DPU_G0065750
myoA
Myosin IA
46917
DPU_G0073894
myoB
Myosin IB
149813
DPU_G0070600
myoC
Myosin IC
34447
DPU_G0054394
myoD
Myosin ID
98367
DPU_G0056238
myoE
Myosin IE
159347
DPU_G0070330
myoF
Myosin IF
149337
DPU_G0068010
myoG
Myosin N
98394
DPU_G0056360
myoH
Myosin H
52275
DPU_G0073054
myoI
Myosin VII
92763
DPU_G0062932
myoJ
Myosin J
25874
DPU_G0073006
myoK
Myosin IK
159515 DPU_G0070836
myoM
Myosin M
Calponin homology domain family
92251
DPU_G0055626
fimA
Fimbrin
149579
DPU_G0069574
Fimbrin-related
protein
99698
DPU_G0067808 fimB/enlA Enlazin/Fimbrin
-2
14945
DPU_G0075678
fimC
Fimbrin-3
100074
DPU_G0072112
fimD
Fimbrin-4
147379
DPU_G0052076
frpA
Fimbrin-related
protein
158441
DPU_G0067794
Fimbrin-related
RasGAP
54845
DPU_G0051436
abpD
Interaptin
91322
DPU_G0060312
abpC
Filamin
47922
DPU_G0053758
abpA
a-actinin
80288
DPU_G0056358
ctxA
Cortexillin 1
58
DDB_G0289585
DDB_G0289585
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
ponA-M
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
Ids in text
hipA
talA
DDB_G0285703
DDB_G0290481
I/LWEQ
I/LWEQ
talB
none
none
none
DDB_G0287505
I/LWEQ, VHP
I/LWEQ
I/LWEQ
I/LWEQ
mhcA
myoA
myoB
myoC
myoD
myoE
myoF
myoG
myoH
myoI
myoJ
myoK
myoM
DDB_G0286355
DDB_G0280039
DDB_G0289117
DDB_G0276617
DDB_G0275447
DDB_G0288679
DDB_G0289177
DDB_G0276363
DDB_G0289447
DDB_G0274455
DDB_G0272112
DDB_G0274575
DDB_G0292262
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
MYO
fimA
none
DDB_G0277855
4xCHf
4xCHf
enlA/fimB
DDB_G0276103
4xCHf
fimC
fimD
frpA
DDB_G0278545
DDB_G0270762
DDB_G0292068
4xCHf
4xCHf
2xCHf
DDB_G0275731
DDB_G0275731
2xCHf
abpD
abpC
abpA
ctxA
FLMN
DDB_G0287291
CH1-CH2
DDB_G0269100 CH1-CH2, FLMN
DDB_G0268632 CH1-CH2, SPEC
DDB_G0289483
CH1-CH2
52744
73997
32330
158954
153438
DPU_G0057754
DPU_G0057590
DPU_G0075670
DPU_G0069126
DPU_G0055442
153591
46997
99638
(no model)
13370
DPU_G0055702
DPU_G0074182
DPU_G0067266
100179
97668
96403
27726
96538
4855
51654
99548
151950
155336
159654
147823
DPU_G0074096
DPU_G0075630
DPU_G0074430
DPU_G0060288
DPU_G0055330
DPU_G0067656
DPU_G0071592
DPU_G0066182
DPU_G0052204
DPU_G0059930
DPU_G0071250
DPU_G0056468
156854
156272
75049
14225
99773
DPU_G0063686
DPU_G0062084
DPU_G0056458
DPU_G0074288
DPU_G0068590
ctxB
Cortexillin 2
gxcCC
RacGEF
gxcAA
gxcDD
NAV/Unc-53related
RacGEF
RacGEF
DPU_G0064322
Smoothelinrelated
ChLim
gxcB
gxcZ
gxcD
gxcBB
gxcA
gefP
pakD
Trix
RacGEF
RacGEF
RacGEF
RacGEF1
RasGEF P
PAK D
Transgelinrelated
eb1
EB1
59
ctxB
DDB_G0294557
gxcCC
DDB_G0287875
DDB_G0284113
DDB_G0276893
DDB_G0294557
DDB_G0279123
DDB_G0287875
DDB_G0284113
CH1-CH2
CH1-CH2
CH1-CH2
CH1-CH2
CH1
gxcAA
gxcDD
DDB_G0280565
DDB_G0283441
DDB_G0272472
DDB_G0282717
DDB_G0279733
DDB_G0280565
DDB_G0283441
DDB_G0272472
CH1
CH1
CH2
CH2
CH2
DDB_G0277777
DDB_G0270220
ChLim
gxcB
gxcZ
gxcD
gxcBB
gxcA
gefP
pakD
DDB_G0289033
DDB_G0292664
DDB_G0277777
DDB_G0270220
DDB_G0267490
DDB_G0269424
DDB_G0293928
DDB_G0267854
DDB_G0277131
DDB_G0277987
DDB_G0281573
DDB_G0269696
DDB_G0289033
DDB_G0292664
CH2
CH3
CH3, LIM
CH3
CH3, VHP
CH3, VHP
CH3
CH3
CH3
CH3
CH3
CH3
DDB_G0269824
DDB_G0267974
DDB_G0282859
none
eb1
DDB_G0269824
DDB_G0267974
DDB_G0282859
CH3
CH3
CH3
CH3
CHe
DDB_G0283607
Figure S12. A phylogenetic tree of the actins of D. purpureum and D. discoideum. The
phylogenetic tree was constructed using the neighbor joining method. D. purpureum and D. discoideum
actins are in blue and red, respectively. The scale bar represents amino acid substitutions per site.
Asterisks indicate groups of identical proteins encoded by different genes.
60
Figure S13. A phylogenetic tree of the ADF domains in D. purpureum and D. discoideum.
The phylogenetic tree was constructed using the neighbor joining method. D. purpureum and D.
discoideum proteins are in blue and in red, respectively. Protein identification numbers are given for D.
purpureum. For D. discoideum non-annotated genes are given as gene identification numbers devoid of
the DDB_G heading. Only the sequences of the ADF domains were used. Domains were aligned
separately in those proteins consisting of duplications or triplications of the domain. The scale bar
represents amino acid substitutions per site. Asterisks denote genes present in two copies in the D.
discoideum genome as the result of the chromosome 2 duplication in the sequenced strain. Underlined are
genes annotated as pseudogenes in the D discoideum genome. D. discoideum cofA and cofB encode an
identical protein but cofB is not expressed. The three major groups of ADF domains are indicated by
different colors of the tree branches and the domain architecture schemes.
Two proteins containing filamin repeats, filamin and filactin (6 and 2 repeats,
respectively) were known previously and are present in both Dictyostelid genomes. We have also
identified two proteins with a single filamin repeat each that are present in both Dictyostelid
species. One protein, 99774 (DPU_G0068600), contains an N-terminal filamin repeat and a Cterminal HECT domain, which is an E3 ubiquitin ligase domain. Proteins with the same domain
61
architecture can be found in insects and chordates, but there is no information on their functional
roles. The other protein, 50592 (DPU_G0065142), consists of leucine-rich repeats and a Cterminal filamin repeat and is apparently unique to Dictyostelium.
Rho signalling
The repertoire of genes encoding proteins that reportedly or presumably participate in Rho
signaling is very similar in both Dictyostelium species (Tables S13 and S14).
Among the Rho effectors, there are three CIP4-related proteins (PCH family) in both species,
after an additional ortholog has been identified in D. discoideum in the course of the present
study. The class of PI4P 5 kinases has undergone a notable expansion in D. purpureum. The D.
discoideum gene DDB_G0286115 is represented by 9 orthologs in D. purpureum, the gene
DDB_G0267588 by two orthologs and one more D. purpureum gene lacks an ortholog in D.
discoideum.
Table S13. Proteins involved in Rho signaling in D. purpureum (summary).
Protein Class
D. purpureum
Genes (No.)
D. discoideum
Genes (No.)
Rho GTPases
Rac-like
3
6
RhoBTB-like
1
1
Other RhoGTPases2 14
14
Dissociation inhibitors
RhoGDI1
1
1
RhoGDI2
1
1
Exchange factors
RhoGEF3
46
47
CZH
8
8
Darlin
1
1
GTPase activating proteins
RhoGAP3
45
46
Effectors and other Rho GTPase-binding proteins
Scar complex
5
5
WASP
1
1
WASP-related
2
2
PAK4
8
9
Gelsolin-related
1
1
Formins
11
10
IQGAP-related
4
4
PCH family
3
3
Lipid kinases5
Phospholipases5
NADPH oxidase
Exocyst complex
LIS1
LimE
25
5
>5
8
1
1
15
5
>5
8
1
1
Relevant domain or
component1
GTPase
GTPase
GTPase
Rac
RhoBTB
Rac (Unique)
RhoGDI
RhoGDI
RhoGDI
RhoGDI (Unique)
RhoGEF (DH)
CZH2 (DHR-2)
Mostly unique
DOCK180, MBC, CED-5
SmgGDS, Yeb3p
RhoGAP
Mostly unique
PIR121
CRIB
CRIB
CRIB
CRIB
GBD
GRD
HR1
WAVE complex
WASP
WASP/WAVE (Unique)
PAK kinases
p85
p67phox
Sec3, Exo70
62
Closest relative(s) in
other organisms
Formins
IQGAP
CIP4, Toca-1, Cdc15p
Class I PI-3-kinases
(p110), PI-4-P5K, DGK
Phospholipase C, D1/2
NADPH oxidase
Exocyst complex
LIS1, Pac1
LIM proteins
The table is based on [53]. Note that for many of the protein families included in the table participation in Rho
signaling has been documented in some species but not in others, therefore a role in Dictyostelium should be
taken as tentative.
1
Relevant domains or components refer, apart from the GTPase, to those involved in interactions with the Rho
GTPase if they have been determined. Abbreviations of the relevant domains: CRIB, Cdcd42 and Rac interactive
binding (also known as PBD, p21-binding domain); CZH2, CDM-zizimin homology 2 domain (also known as
DHR-2, Dock homology region 2); GAP, GTPase activating protein; GBD, Rho GTPase-binding domain of
formins; GDI, guanine nucleotide dissociation inhibitor; GEF, guanine nucleotide exchange factor (the RhoGEF
domain is also known as DH, Dbl homology domain); GRD, RasGAP-related domain; HR1, protein kinase Crelated kinase homology region 1.
2
In D.discoideum this group includes RacC to E, RacG to Q and the pseudogene RacK. In D. purpureum this
group includes RacC to E, RacG, RacH, RacJ, RacL, RacP and RacR to RacW.
3
Three genes encode proteins with both RhoGAP and RhoGEF domains.
4
In D. discoideum PakH exists as two copies, one on the chromosome 2 duplication
5
Includes 6 PI3 kinases (p110 subunit), one DAG kinase and 9 (in D. discoideum) or 18 (in D purpureum) PI-4P5 kinase genes. The p85 regulatory subunit of the PI3 kinase, which in vertebrates interacts with Cdc42 and
Rac1, is apparently missing in D. discoideum and D. purpureum. This does not exclude a potential regulation by
Rho GTPases through other mechanisms, therefore PI 3-kinases have not been excluded from the table.
6
Includes a single phospholipase C as well four phospholipase D proteins related to mammalian PLD1 and
PLD2.
Table S14. Proteins involved in Rho signaling in D. purpureum (detail).
D. purpureum
Protein ID
Rho GTPases
92985
168754#
50894
168757#
55703
93635#
98135
75463
41217
147341
52376
89172
80321#
81024#
149292
81474
81475
158834
RhoGDI
95353
78427
RhoGEF (DH)
99548
27726
156926
4855
D. purpureum
dictyBase Gene I.D.
Proposed
D. purpureum
gene name
D. discoideum
dictyBase Gene ID
D. discoideum
Ortholog
DPU_G0066198
DPU_G0057068
DPU_G0066986
DPU_G0061650
DPU_G0054880
DPU_G0058262
DPU_G0054576
DPU_G0060756
DPU_G0065542
DPU_G0051392
DPU_G0075220
DPU_G0060224
DPU_G0056546
DPU_G0058588
DPU_G0067766
DPU_G0059740
DPU_G0059742
DPU_G0068822
rac1a1
rac1a2
racA
racB
racC
racD
racE
racG
racH
racJ
racL
racP
racR
racS
racT
racU
racV
racW
DDB_G0277869
DDB_G0277869
DDB_G0286555
DDB_G0279605
DDB_G0293526
DDB_G0291976
DDB_G0280975
DDB_G0269178
DDB_G0269240
DDB_G0292560
DDB_G0292816
DDB_G0285453
rac1a
rac1a
racA
racB
racC
racD
racE
racG
racH
racJ
racL
racP
DPU_G0061434
DPU_G0051684
rdiA
rdiB
DDB_G0291077
DDB_G0280049
rdiA
rdiB
DPU_G0066182
DPU_G0060288
DPU_G0063820
DPU_G0067656
gxcA
gxcB
gxcC
gxcD
DDB_G0277987
DDB_G0269424
DDB_G0284845
DDB_G0267854
gxcA
gxcB
gxcC
gxcD
63
DPU_G0059622
81422
DPU_G0071806
85191
DPU_G0055688
153584
DPU_G0071818
77025
DPU_G0071828
77030
DPU_G0055350
45161
DPU_G0061232
148367
DPU_G0064952
83267
DPU_G0064972
148839
DPU_G0072848
96166
DPU_G0052190
97823
DPU_G0065600
41248
DPU_G0059456
155148
DPU_G0064124
89777
DPU_G0062438
82447
DPU_G0069476
84596
DPU_G0052094
26275
DPU_G0053238
33732
DPU_G0055058
153285
DPU_G0066958
158102
DPU_G0063332
39928
DPU_G0055330
96538
DPU_G0055702
153591
DPU_G0071592
51654
DPU_G0075670
32330
DPU_G0074182
46997
DPU_G0061832
82194
DPU_G0053642
152605
DPU_G0065484
92938
DPU_G0064668
148817
DPU_G0061516
99010
DPU_G0063228
99199
DPU_G0055312
26788
DPU_G0065986
157827
DPU_G0069236
52129
DPU_G0063182
148631
DPU_G0066114
157834
DPU_G0070836
159515
DPU_G0053802
79261
RhoGEF (Dock180 and ELMO)
DPU_G0051892
47503
DPU_G0054908
34798
DPU_G0060636
81789
DPU_G0061656
27977
DPU_G0052276
151994
DPU_G0056004
153700
DPU_G0053332
152501
DPU_G0070224
149722
DPU_G0057496
96234
DPU_G0066098
86597
DPU_G0067304
50960
gxcE
gxcF
gxcG
gxcH
gxcI
gxcJ
gxcK
gxcL
gxcM
gxcN
gxcO
gxcP
gxcQ
gxcR
gxcS
gxcT
gxcU
gxcV
gxcW
gxcX
gxcY
gxcZ
gxcAA
gxcBB
gxcCC
gxcDD
gxcEE
gxcFF
gxcGG
gxcHH
gxcII
gxcJJ
gxcKK
kxcA
kxcB
roco5
gefC
myoM
DDB_G0291085
DDB_G0282475
DDB_G0282073
DDB_G0288377
DDB_G0288383
DDB_G0293978
DDB_G0291007
DDB_G0290023
DDB_G0272372
DDB_G0277017
DDB_G0293396
DDB_G0285859
DDB_G0284501
DDB_G0285303
DDB_G0280087
DDB_G0269610
DDB_G0291996
DDB_G0282271
DDB_G0278147
DDB_G0274889
DDB_G0293266
DDB_G0293928
DDB_G0282717
DDB_G0277131
DDB_G0279123
DDB_G0279733
DDB_G0281047
DDB_G0284739
DDB_G0268354
DDB_G0290493
DDB_G0278703
DDB_G0275679
DDB_G0293340
DDB_G0289859
DDB_G0293124
DDB_G0294533
DDB_G0282381
DDB_G0292262
DDB_G0269934
gxcE
gxcF
gxcG
gxcH
gxcI
gxcJ
gxcK
gxcL
gxcM
gxcN
gxcO
gxcP
gxcQ
gxcR
gxcS
gxcT
gxcU
gxcV
gxcW
gxcX
gxcY
gxcZ
gxcAA
gxcBB
gxcCC
gxcDD
gxcEE
gxcFF
gxcGG
gxcHH
gxcII
gxcJJ
gxcKK
kxcA
kxcB
roco5
gefC
myoM
DDB_G0269934
docA
docB
docC
docD
zizA
zizB
zizC
zizD
elmoA
elmoB
elmoC
DDB_G0291974
DDB_G0270404
DDB_G0292004
DDB_G0284725
DDB_G0275035
DDB_G0293084
DDB_G0275239
DDB_G0268888
DDB_G0278051
DDB_G0280179
DDB_G0282949
docA
docB
docC
docD
zizA
zizB
zizC
zizD
elmoA
elmoB
elmoC
64
99508
94211
76775
Darlin
40381
RhoGAP
29142
96526
(no model)
82068
153891
146520
(no model)
147510
50285
89900
93648
95356
88032
158397
10267
155202
158606
85916
158993
97430
98229
98974
15574
150164
159700
97170
56354
155654
15662
42386
149424
149898
98143
77981
153400
98122
96792
150174
148693
40694
4417
77513
RhoGEF + RhoGAP
96450
154253
DPU_G0065782
DPU_G0073680
DPU_G0070396
elmoD
elmoE
elmoF
DDB_G0280943
DDB_G0279657
DDB_G0267548
elmoD
elmoE
elmoF
DPU_G0064106
darA
DDB_G0288771
darA
DPU_G0067174
DPU_G0054746
gacA
gacB
gacC
gacD
gacE
gacF
gacG
gacH
gacI
gacJ
gacK
gacL
gacM
gacN
gacO
gacP
gacQ
gacR
gacS
gacT
gacU
gacV
gacW
gacX
gacY
gacZ
mgp3/mpgAA
mgp1/mpgBB
mgp2/gacCC
mgp4/gacDD
gacEE
gacFF
gacGG
gacHH
gacJJ
Dp5p4
DDB_G0278381
DDB_G0278549
DDB_G0284571
DDB_G0291021
DDB_G0293654
DDB_G0274243
DDB_G0283955
DDB_G0272694
DDB_G0275185
DDB_G0285641
DDB_G0285915
DDB_G0290891
DDB_G0287895
DDB_G0279315
DDB_G0267568
DDB_G0279009
DDB_G0282395
DDB_G0278755
DDB_G0276833
DDB_G0285163
DDB_G0272925
DDB_G0293510
DDB_G0290439
DDB_G0288205
DDB_G0281739
DDB_G0269496
DDB_G0269624
DDB_G0290233
DDB_G0270024
DDB_G0270024
DDB_G0289667
DDB_G0286773
DDB_G0279569
gacA
gacB
gacC
gacD
gacE
gacF
gacG
gacH
gacI
gacJ
gacK
gacL
gacM
gacN
gacO
gacP
gacQ
gacR
gacS
gacT
gacU
gacV
gacW
gacX
gacY
gacZ
gacAA
gacBB
mgp2/gacCC
mgp4/gacDD
gacEE
gacFF
gacGG
gacHH
gacJJ
Dd5p4
DDB_G0293184
roco9
roco10
gefD
gflB
gflD
DDB_G0291978
DDB_G0278417
xacA
xacB
DPU_G0061452
DPU_G0056322
DPU_G0051180
DPU_G0053436
DPU_G0063832
DPU_G0064892
DPU_G0058818
DPU_G0061454
DPU_G0053702
DPU_G0067616
DPU_G0053570
DPU_G0059558
DPU_G0068154
DPU_G0051352
DPU_G0069188
DPU_G0073602
DPU_G0055212
DPU_G0061350
DPU_G0055276
DPU_G0072142
DPU_G0071574
DPU_G0070034
DPU_G0057264
DPU_G0060628
DPU_G0066588
DPU_G0068110
DPU_G0068558
DPU_G0070966
DPU_G0054624
DPU_G0075120
DPU_G0055260
DPU_G0054482
DPU_G0062136
DPU_G0072160
DPU_G0063892
DPU_G0064598
DPU_G0061560
DPU_G0073816
DPU_G0052100
DPU_G0057146
roco9
roco10
gefD
gflB
gflD
xacA
xacB
65
DDB_G0291840
DDB_G0275085
DDB_G0280093
DDB_G0272080
DDB_G0290873
DDB_G0267462
DDB_G0293184
DDB_G0288183
DDB_G0291710
DPU_G0067748
86690
Effectors with CRIB/PBD
DPU_G0072896
87126
DPU_G0059876
81492
(no model)
DPU_G0071952
90830
DPU_G0062510
96263
DPU_G0074072
31335
DPU_G0074390
91113
DPU_G0059930
155336
DPU_G0072662
44150
DPU_G0074510
150846
DPU_G0056426
147802
DPU_G0065958
90051
Scar complex
DPU_G0065084
40920
DPU_G0053536
87985
DPU_G0071848
46589
DPU_G0056120
153775
DPU_G0054936
88267
Formins
DPU_G0073676
150581
DPU_G0053232
33735
DPU_G0066776
50865
DPU_G0073848
46912
DPU_G0057262
154316
DPU_G0059834
148204
DPU_G0056158
153797
DPU_G0063964
156963
DPU_G0056740
36102
DPU_G0070450
97202
DPU_G0062882
99159
IQGAP
DPU_G0069466
42926
DPU_G0060430
49582
DPU_G0067794
158441
DPU_G0073888
31268
Effectors with HR1 domain
DPU_G0053940
152774
DPU_G0052560
92017
DPU_G0055482
48387
PI3 kinases
58194
52203
149892
155819
35373
96754
PI4P 5 kinases
52460
148173
DPU_G0065578
DPU_G0071394
DPU_G0070956
DPU_G0061026
DPU_G0055696
DPU_G0061222
xacC
DDB_G0285391
xacC
wasA
DDB_G0293834
DDB_G0272811
DDB_G0283827
DDB_G0276571
wasA
DDB_G0272811
DDB_G0283827
gnrC
pakA
pakB
pakC
pakD
pakE
pakF
pakG
pakH
DDB_G0269166
DDB_G0276459
DDB_G0267450
DDB_G0269696
DDB_G0293932
DDB_G0274409
DDB_G0282891
DDB_G0269166
gnrC
pakA
pakB
pakC
pakD
pakE
pakF
pakG
pakH
scrA
abiA
pirA
napA
hspc300
DDB_G0285253
DDB_G0267956
DDB_G0287855
DDB_G0274519
DDB_G0279175
scrA
abiA
pirA
napA
hspc300
forA
forB
forC
forD
forE
forF
forG
forH
forI
forJ
forK
DDB_G0279607
DDB_G0282297
DDB_G0287295
DDB_G0282245
DDB_G0269626
DDB_G0289763
DDB_G0277175
DDB_G0285589
DDB_G0284519
DDB_G0291378
forA
forB
forC
forD
forE
forF
forG
forH
forI
forJ
none
gapA
rgaA
DDB_G0269140
DDB_G0287585
DDB_G0275731
DDB_G0288977
gapA
rgaA
DDB_G0275731
DDB_G0288977
DDB_G0271812
DDB_G0271676
DDB_G0274695
DDB_G0271812
DDB_G0271676
DDB_G0274695
DDB_G0278727
DDB_G0283081
DDB_G0275011
DDB_G0289601
DDB_G0282625
DDB_G0291093
pikA
pikB
pikC
pikE
pikG
pikH
DDB_G0280377
DDB_G0286115
DDB_G0280377
DDB_G0286115
pikA
pikB
pikC
pikE
pikG
pikH
DPU_G0052116
DPU_G0059774
66
148780
97761
82538
157566
41242
84210
159799
160088
55653
82999
154611
37984
57810
99415
DPU_G0064312
DPU_G0051730
DPU_G0062938
DPU_G0065446
DPU_G0065592
DPU_G0068074
DPU_G0071882
DPU_G0072838
DPU_G0054650
DPU_G0064208
DPU_G0058136
DPU_G0059910
DPU_G0063860
DPU_G0064944
DPU_G0072414
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0267588
DDB_G0267588
DDB_G0292190
DDB_G0275635
DDB_G0279149
DDB_G0283615
DDB_G0274067,
DDB_G0272638
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0286115
DDB_G0267588
DDB_G0267588
DDB_G0292190
PIPkinA
pip5k3
rpkA
DDB_G0274067,
DDB_G0272638
none
dgkA
DDB_G0277223
dgkA
pldA
pldB
pldC
DDB_G0281031
DDB_G0279483
DDB_G0277949
DDB_G0284155
pldA
pldB
pldC
DDB_G0284155
pipA
DDB_G0292736
plc/pipA
ncfA
noxA
noxB
noxC
cybA
DDB_G0288773
DDB_G0289653
DDB_G0287101
DDB_G0291117
DDB_G0267460
ncfA
noxA
noxB
noxC
cybA
DPU_G0060854
DPU_G0063716
DPU_G0061340
DPU_G0057344
DPU_G0065644
DPU_G0062970
DPU_G0055210
DPU_G0059426
sec3/exoc1
sec5/exoc2
sec6/exoc3
sec8/exoc4
sec10/exoc5
sec15/exoc6
exo70/exoc7
exo84/exoc8
DDB_G0285067
DDB_G0280081
DDB_G0293520
DDB_G0284833
DDB_G0287881
DDB_G0293936
DDB_G0272991
DDB_G0279991
sec3/exoc1
sec5/exoc2
sec6/exoc3
sec8/exoc4
sec10/exoc5
sec15/exoc6
exo70/exoc7
exo84/exoc8
DPU_G0054034
DPU_G0071820
limE
lis1
DDB_G0279415
DDB_G0288375
limE
lis1
159970
DPU_G0071608
85137
DAG kinases
DPU_G0057790
147968
Phospholipase D
DPU_G0067580
95839
DPU_G0067132
149141
DPU_G0055620
55934
DPU_G0059446
218575#
Phospholipase C
DPU_G0055284
96532
NADPH oxidase complex
DPU_G0064096
99304
DPU_G0075352
32111
DPU_G0065620
41266
DPU_G0073618
51890
DPU_G0070392
30041
Exocyst complex
89267
50260
155933
36520
28786
89602
88329
37625
Others
94684
46585
PIPkinA
pip5k3
rpkA
#alternative JGI models replacing models originally selected for the Gene Catalog.
67
Figure S14. Phylogenetic tree of the Rho family in D. purpureum and D. discoideum.
Complete sets of Rho proteins from several species were used. This comprises the 18 D. purpureum Rho
proteins(in blue), the 21 D. discoideum Rho proteins (including a reconstructed sequence of RacK) (red),
6 from Saccharomyces cerevisiae (Sc), 5 from Caenorhabditis elegans (Ce), 7 from Drosophila
melanogaster (Dm) and 20 from Homo sapiens (Hs). Human RhoBTB3 was not included in the analysis,
as its GTPase domain is strongly erased. The phylogenetic tree was constructed using the neighbor
68
joining method with the core GTPase domain devoid of N- and C-terminal repetitive sequences.
Bootstraps between homonymous proteins of D. purpureum and D. discoideum are not indicated; they
were 100% in all cases. Dictyostelium has representatives of the Rac subfamily, but lacks Rho and Cdc42
proteins. Note that the RacA GTPase domain is more closely related to Rac proteins than to RhoBTB
proteins, although RacA has the domain architecture of a RhoBTB protein. The scale bar indicates amino
acid substitutions per site.
The Ras superfamily of GTPases
The Ras superfamily of GTPases. This group comprises classical “small GTPases” and
their relatives (the GTPase component of heterotrimeric G-proteins, multidomain ROCO
proteins etc.). These proteins generally function as critical regulators of a diverse array of
cellular processes (signaling cascades, membrane trafficking, cytoskeleton dynamics etc.), hence
the elaboration of the Ras superfamily correlate with the organismal and cell complexity.
Comparison of the Ras superfamily complement in D. purpureum and D. discoideum can be
found in Table S15 and Figures S15-S17. The D. purpureum genome encodes fewer superfamily
members (150, versus 175 in D. discoideum). This difference appears to be due to less extensive
gene duplication and more extensive gene loss in the D. purpureum lineage. Nevertheless, there
is a one-to-one orthologous correspondence between most Ras superfamily GTPases from D.
purpureum and D. discoideum. Notable exceptions in the form of independent family expansions
include, in addition to those described above for the Rho family, six Ras family (rasU to rasZ)
corresponding to just one gene in D. purpureum (DPU_G0070892; Figure S15). A lot of
independent evolution is particularly seen in the Rab family of vesicle trafficking regulators
(Figure S16), suggesting that there might be substantial differences between the two species in
the organization and function of the endomembrane system.
Table S15. The Ras superfamily of GTPases in D. purpureum and D. discoideum.
D. purpureum
Proposed
Protein model
dictyBase Gene
D. discoideum
Gene namec
69
notes
dictyBase Gene
gene namea IDb
IDc
RAS family
rheb
rapA
rapB
rapC
rasB
rasC
rasD
rasG
rasS
NA
147775
59134
26434
74092#
47179
51488
91367
92731
57324
93239
DPU_G0055948
DPU_G0071072
DPU_G0053506
DPU_G0062576
DPU_G0075064
DPU_G0070498
DPU_G0062120
DPU_G0062342
DPU_G0061508
DPU_G0070892
90155#
79073#
84962#
55232
CBTG1621.b1
(EST
sequence;
absent from
the genome
assembly but
recorded by
several
unassembled
reads)
DPU_G0066746
DPU_G0053296
DPU_G0070728
DPU_G0052952
rsmA
rsmB
rsmD
NA
NA
IDc
rheb
rapA
rapB
rapC
rasB
rasC
rasD
rasG
rasS
rasU
rasV
rasW
rasX
rasY
rasZ
rsmA
rsmB
rsmC
rsmD
rsmE-1
rsmE-2
DDB_G0277041
DDB_G0291237
DDB_G0272857
DDB_G0270340
DDB_G0292998
DDB_G0281385
DDB_G0292996
DDB_G0293434
DDB_G0283537
DDB_G0270138
DDB_G0270736
DDB_G0270122
DDB_G0270124
DDB_G0270126
DDB_G0270140
DDB_G0283547
DDB_G0281253
DDB_G0278449
DDB_G0292318
DDB_G0273099
DDB_G0273825
NA
168758$
rsmF
rsmG
rsmH
rsmJ
rsmK
DPU_G0052626 DDB_G0280437
-
-
-
NA
96273
DPU_G0062638 DDB_G0270932
cpras1
168760$
DPU_G0073460 cpras1
cpras2
80287#
DPU_G0056356 cpras2
DDB_G0293786
RAB family
70
Independent family
expansion in D.
discoideum (six
paralogs)
Very divergent
Possibly independent
family expansions in
D. purpureum (two
paralogs) and D.
discoideum (seven
paralogs)
DDB_G0278389
DDB_G0278717
DDB_G0278403
DDB_G0279305
DDB_G0278217
DDB_G0280437 Uncharacterised
RAS-like GTPase
DDB_G0293786 Uncharacterised D.
discoideum-specific
RAS-like GTPase
DDB_G0270932 Two tandemly
arranged divergent
RAS-like domains
DDB_G0277381 Circularly-permuted
RAS-like domain
(cpRAS) protein
DDB_G0293376 Circularly-permuted
RAS-like domain
(cpRAS) protein
rab1A
rab1B
rab1C
rab1D
-
159642
50297
97759
54449
-
rab2A
rab2B
rab4A
rab4B
rab4C
rab5A
rab5B
rab6
rab7A
rab7B
rab8
92882
96118*
41201
26958
39631
93331
86102
52877
92126
78083
91938
rab11A
DPU_G0071228
DPU_G0063876
DPU_G0051726
DPU_G0074050
-
DDB_G0283757
DDB_G0277867
DDB_G0269174
DDB_G0284985
DDB_G0275969
DDB_G0282203
DDB_G0292268
DDB_G0272138
DDB_G0292406
91321#
rab1A
rab1B
rab1C
rab1D
rab1E
rabY
DPU_G0064540 rab2A
DPU_G0071958 rab2B
DPU_G0065550 rab4
DPU_G0056408
DPU_G0062856
DPU_G0073260 rab5A
DPU_G0056432 rab5B
DPU_G0059370 rab6
DPU_G0054224 rab7A
DPU_G0075452 rab7B
DPU_G0051692 rab8A
rab8B
DPU_G0060304 rab11A
rab11C
rab14
rab18
rab21
rab24
rab32A
rab32A2_p
s
96604
92215
57208
54865
78440
74712
147455
DPU_G0057776
DPU_G0055130
DPU_G0060976
DPU_G0051534
DPU_G0051710
DPU_G0052764
DPU_G0052760
rab32B
rab32C
rab32D
rabC
rabG
148238
91127
46949*
47972
96892
DPU_G0060276
DPU_G0051274
DPU_G0074000
DPU_G0053946
DPU_G0064676
rabJ
rabQ
-
156394
82365
-
-
-
DDB_G0287211
DDB_G0277101
DDB_G0281337
DDB_G0289827
DDB_G0286553
DDB_G0268402
DDB_G0283603 Local gene
duplication in D.
purpureum
comprising an intact
gene and an adjacent
apparent pseudogene
DDB_G0269416
DDB_G0275675
DDB_G0285051
DDB_G0271736
DDB_G0291738
DDB_G0290783
DDB_G0275955
DDB_G0277441
DDB_G0268760
DDB_G0291233
DDB_G0272905
DDB_G0273935
DDB_G0276053 pseudogene
DDB_G0290833 Large family
DDB_G0290791 expansion of
DDB_G0290831 divergent Rab7DDB_G0290779 related paralogs in D.
DDB_G0290829 discoideum (11 loci,
DDB_G0290789 some may be
DDB_G0290793 pseudogenes),
DDB_G0294571 without orthologs in
DDB_G0290827 D. purpureum
DDB_G0271984
DDB_G0282847
DDB_G0268068
DDB_G0269236
DDB_G0287553
DDB_G0280043
DDB_G0276399
DDB_G0269238
rab11B
rab11C
rab14
rab18
rab21
rab24
rab32A
rab32B
rab32C
rab32D
rabC
rabG1
rabG2
rabH
DPU_G0062380 rabJ
DPU_G0062272 rabQ
rabA
rabF1-1
rabF1-2
rabF2_ps
rabK1
rabK2
rabK3
rabL
rabM
rabN1
rabN2
DDB_G0294571
DDB_G0290827
71
rabS
-
160488*
-
NA
77270#
rabO
rabP
DPU_G0074528 rabS
rabR
rabT1
rabT2
DDB_G0294583
DDB_G0294569
rabU
DPU_G0072786 rabV
NA
82173
DPU_G0061790 rabW
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
152785
78832#
83134#
74151#
78917
84758#
75757
73840
75864
148542
36395
80610#
168762$
37398
79526#
38803
38788
39890
25125
DPU_G0053958
DPU_G0052616
DPU_G0064588
DPU_G0066374
DPU_G0052950
DPU_G0070090
DPU_G0063172
DPU_G0051070
DPU_G0064250
DPU_G0062744
DPU_G0057254
DPU_G0057246
DPU_G0057252
DPU_G0059062
DPU_G0054478
DPU_G0061312
DPU_G0061314
DPU_G0063268
DPU_G0057494
rabX
rabZ
DDB_G0276007
-
-
-
RHO family
rac1A1
rac1A2
racA
racB
racC
racD
racE
-
92985
168754$
50894
168757*$
55703
93635#
98135
-
DPU_G0066198
DPU_G0057068
DPU_G0066986
DPU_G0061650
DPU_G0054880
DPU_G0058262
DPU_G0054576
-
rac1A
DDB_G0277869
racG
racH
-
75463
41217
-
rac1B
rac1C
racA
racB
racC
racD
racE
racF1
racF2
DPU_G0060756 racG
DPU_G0065542 racH
racI
DDB_G0268622
DDB_G0282365
DDB_G0286555
DDB_G0279605
DDB_G0293526
DDB_G0291976
DDB_G0280975
DDB_G0269176
DDB_G0276967
DDB_G0269178
DDB_G0269240
DDB_G0277897
72
DDB_G0290407
DDB_G0290875
DDB_G0282537
DDB_G0271980
DDB_G0268910
DDB_G0269262
DDB_G0294583
DDB_G0294569
DDB_G0291293
DDB_G0282899 Orthology between
D. purpureum and D.
discoideum unsure
DDB_G0276295 Orthology between
D. purpureum and D.
discoideum unsure
DDB_G0275327 Extremely divergent
DDB_G0286169
DDB_G0276007
Not completely sure
that all these paralogs
have a common
origin (rather
divergent sequences,
some may be
pseudogenes)
Not completely sure
that all these paralogs
have a common
origin (rather
divergent sequences)
racJ
racL
racP
racR
racS
racT
racU
racV
racW
NA
147341
52376
89172
80321#
81024#
149292
81474
81475
158834
49642
DPU_G0051392
DPU_G0075220
DPU_G0060224
DPU_G0056546
DPU_G0058588
DPU_G0067766
DPU_G0059740
DPU_G0059742
DPU_G0068822
DPU_G0060690
racJ
racK_ps
racL
racP
racM
racN
racO
racQ
ARF/Sar1
family
arfA
NA
NA
93077
46140
75970
DPU_G0067816 arfA
DPU_G0068504 DPU_G0065016
arl1
arl2
arl5
arl8
arfrp1
arrB
arrC
arrD
NA
NA
NA
NA
NA
81368
90855*
93016
93516#
86826#
77595
41641
35934
73266
73423
87458
38752
79687
DPU_G0059512
DPU_G0072228
DPU_G0066824
DPU_G0052688
DPU_G0069592
DPU_G0074070
DPU_G0066606
DPU_G0056396
DPU_G0063870
DPU_G0066132
DPU_G0075268
DPU_G0061148
DPU_G0054922
NA
92653
DPU_G0061354 -
arrL
-
150230
-
DPU_G0072342 arrL
DDB_G0292332
NA
147576
DPU_G0054126 DDB_G0278443
sarA
sarB
46167
168733$
DPU_G0068760 sarA
DPU_G0068040 sarB
DDB_G0282605
arl1
arl2
arl5
arl8
arfrp1
arrA
arrB
arrC
arrD
arrE
arrF
arrG_ps
arrH
arrJ
arrK
G-alpha family (a subunit of heterotrimeric G-proteins)
gpaA
53968
DPU_G0071128 gpaA
gpaB
91607
DPU_G0070624 gpaB
DDB_G0292560
DDB_G0268908
DDB_G0292816
DDB_G0285453
DDB_G0289103
DDB_G0278009
DDB_G0277791
DDB_G0278011
Independent family
expansions in D.
purpureum (six
paralogs) and D.
discoideum (four
paralogs)
DDB_G0282605 Divergent RHO-like
domain fused to a
LRR domain
DDB_G0289173
Seems to be D.
purpureum-specific
divergent paralogs of
arfA (lacking the Nterminal
myristoylation motif)
DDB_G0288163
DDB_G0281307
DDB_G0271942
DDB_G0283525
DDB_G0283631
DDB_G0282457
DDB_G0274445
DDB_G0271792
DDB_G0289069
DDB_G0280479 Possibly independent
DDB_G0289435 family expansions in
DDB_G0280697 D. purpureum (five
DDB_G0288015 paralogs) and D.
DDB_G0280621 discoideum (five
DDB_G0280633 paralogs and a
pseudogene)
Uncharacterised D.
purpureum-specific
ARF-like GTPase
DDB_G0278057
DDB_G0292332 Uncharacterised D.
discoideum-specific
ARF-like GTPase
DDB_G0278443 Uncharacterised
ARF-like GTPase
DDB_G0272296
DDB_G0278477
DDB_G0283349
DDB_G0276267
73
pseudogene
gpaC
gpaD
gpaE
gpaF
gpaG
gpaH
gpaI
gpaK
gpaL
spnA
gbqA
159561
93271
149474*#
93749#
92301
91506
36694
92510
150924
160336
153084
DPU_G0071010
DPU_G0071740
DPU_G0068812
DPU_G0061752
DPU_G0056224
DPU_G0068236
DPU_G0057962
DPU_G0059260
DPU_G0074682
DPU_G0073856
DPU_G0054594
gpaC
gpaD
gpaE
gpaF
gpaG
gpaH
gpaI
gpaJ
gpaK
gpaL
spnA
gbqA
DDB_G0287031
DDB_G0285425
DDB_G0286185
DDB_G0283151
DDB_G0276455
DDB_G0284469
DDB_G0283419
DDB_G0268802
DDB_G0276343
DDB_G0280351
DDB_G0276155
DDB_G0280965
Other Ras superfamily GTPases
ranA
150415#
DPU_G0073176 ranA
ranB
29152#
DPU_G0067138 ranB
spg1
gemA
srpRB
NA
94854#
168763*$
147655
150131#
ragA
ragC
NA
35824
80421*
159388#
dync1li1
comB
NA
34712
146844*
CCAB688.g1
(EST
sequence,
absent from
the genome
assembly)
NA
83633#
NA
84055
DDB_G0291235
DDB_G0274943 D. discoideum
protein has two
RAN-like domains,
while D. purpureum
protein has only one
(corresponding to the
C-terminal domain of
the former)
DPU_G0055742 spg1
DDB_G0291269
DPU_G0071886 gemA
DDB_G0267830
DPU_G0054742 srpRB
DDB_G0278543
DPU_G0072010 DDB_G0286513 DDB_G0286513 Ortholog of
Arabidopsis LIP1
and human RABL3
DPU_G0056242 ragA
DDB_G0288701
DPU_G0056746 ragC
DDB_G0284495
DPU_G0070482 DDB_G0270744 DDB_G0270744 Ortholog of human
RBEL1
DPU_G0054794 dync1li1
DDB_G0292904
DPU_G0066452 comB
DDB_G0281825
DDB_G0282647 DDB_G0282647 Uncharacterised
GTPase, may be
divergent member of
the RAB family (but
lacks a C-terminal
prenylation motif),
related to
DDB_G0294577
DPU_G0066126 DDB_G0294577 DDB_G0294577 Uncharacterised
DDB_G0282649_ DDB_G0282649 GTPase, may be
divergent member of
ps
the RAB family (but
lacks a C-terminal
prenylation motif),
related to
DDB_G0282647
DPU_G0067564 DDB_G0276227 DDB_G0276227 Divergent RAB-like
GTPase domain
fused with a LRR
domain
74
rsmM
89854
DPU_G0064544 rsmM
-
-
-
NA
97732
DPU_G0051548 DDB_G0287061
-
-
DDB_G0287207
NA
Absent from
the genome
assembly but
recorded by
several
unassembled
reads
(FFAS169538.
g1,
FFAS99606.b
1…)
DDB_G0274301
rsmN
DDB_G0282653
DDB_G0292300 Perhaps should be
classified as a
divergent member of
the RAB family
DDB_G0282651 These two genes
DDB_G0282653 seems to form a D.
discoideum-specific
family of divergent
GTPases
DDB_G0287061 Large
uncharacterised
protein with a
divergent C-terminal
GTPase domain;
related to
DDB_G0287207
DDB_G0287207 Large
uncharacterised
protein with a
divergent C-terminal
GTPase domain;
related to
DDB_G0287061
DDB_G0274301 Divergent RAB-like
GTPase domain
protein
ROCO family (containing Roc GTPase domain)
pats1
159478*
DPU_G0070698 pats1
DDB_G0269250
qkgA-1
DDB_G0273259
qkgA-2
DDB_G0273635
gbpC
168746$
DPU_G0059624 gbpC
DDB_G0291079
roco4
49056
DPU_G0058498 roco4
DDB_G0288251
roco5
148631
DPU_G0063182 roco5
DDB_G0294533
roco6
99455#
DPU_G0065240 roco6
DDB_G0279417
roco7
81310
DPU_G0059300 roco7
DDB_G0267472
roco8
56686#
DPU_G0058976 roco8
DDB_G0286127
roco9
150174
DPU_G0072160 roco9
DDB_G0288183
roco10
96855#
roco10
DDB_G0291710
roco11
DDB_G0268636
Individual rows or series of consecutive rows separated by black lines correspond to inferred orthologous groups of
genes between D. purpureum and D. discoideum (based on BLASTP searches and phylogenetic analyses, see
Figures S15, S16 and S17). Rows separated by grey lines comprise lineage-specific paralogs presumably originating
from gene duplications that occurred independently in D. purpureum or D. discoideum lineages. Dashes indicate
absence of discernible orthologs in one or the other species, either due to gene loss or potentially due to technical
limitations (e.g. too extensive divergence) precluding inference of actual orthologous relationships.
a
Gene names proposed following names of unambiguous D. discoideum orthologs; NA – name not assigned.
75
b
JGI Dictyostelium purpureum QSDP1 protein models [13].
Official D. discoideum gene names and corresponding protein IDs taken from dictyBase [14].
*loci affected by a gap or an error in the genome assembly.
#alternative JGI models replacing models originally selected for the Gene Catalog.
$new models created by modification of existing JGI models.
c
76
Figure S15. Phylogenetic analysis of the Ras family in D. discoideum and D. purpureum. The tree
was inferred from an alignment constructed with the aid of ClustalX and extensive manual curation.
Ambiguously aligned positions were discarded and the remaining positions were subjected to maximum
likelihood tree search using RAxML 7.0.4 (WAG+4+I+F substitution model) and the rapid
bootstrapping algorithm (100 bootstrap replicates, branch support values shown only when higher than
50). Sequences that were too divergent and pseudogenes were excluded from the analysis.
77
Figure S16. Phylogenetic analysis of the Rab family in Dictyostelium spp. For methodical details see
the legend of Figure S15.
78
Figure S17. Phylogenetic analysis of the ARF/Sar1 family in Dictyostelium spp. For methodical
details see the legend of Figure S15.
79
The D. pupureum Glycome
Comparison of predicted protein sequences of D. purpureum with the CAZy classification [55]
[56] of known glycosyltransferases (GTs), glycohydrolases (GHs), carbohydrate binding
modules which are appended to enzyme domains (CBMs), esterases, and expansins are all
described in supplemental Table S16. The predicted D. purpureum proteins were searched for
sequences that could be classified according to the CAZy scheme of glycosyltransferases,
glycohydrolases, carbohydrate-binding modules associated with the above, carbohydrate
esterases which modify glycans, and expansins. Additional sequences related to
glycophosphotransferases, carbohydrate-binding domains (not typically associated with
glycoenzymes), and extracellular matrix proteins (some of which have cellulose-binding activity)
are also included (denoted as “other”). Proteins with multiple domains fitting these criteria are
counted multiple times. Duplicate genes resulting from chromosomal duplications in axenic
strains are not counted. Genes within each class are enumerated in Tables S17, S18, and S19 as
indicated.
Storage carbohydrates. The cytoplasm is also the site of accumulation of glycogen, an glucan polysaccharide that serves as a nutritional store and whose abundance influences cell fate
within the slug. Glycogen synthesis and metabolizing enzymes have been described in D.
discoideum [54], but gene predictions suggest distinctive features that are not fully understood.
Both D. discoideum and D. purpureum lack glycogenin, the primer and initiating
glucosyltransferase of glycogen synthesis in animals, plants and fungi, though yeast can
synthesize glycogen in the absence of glycogenin [126]. In addition to a conventional family
GT3 glycogen synthase-like gene, D. discoideum and D. purpureum each have a related family
GT5 starch synthase-like gene that is similar to that of glaucophytes and red algae, and a GH77
4--glucanotransferase (transglycosidase)-like gene [127]. However, other genes associated with
80
starch metabolism are lacking raising the possibility that these genes have unknown alternative
functions. Trehalose is a second storage carbohydrate that accumulates to a high level in spores
where it may stabilize proteins during desiccation and provide nutrition after germination [128].
D. discoideum and D. purpureum each have genes associated with trehalose metabolism (GH15,
GH37, GH65 and GT20 families) indicative of use of a eukaryotic rather than a prokaryote-type
pathway (Table S18).
Cellulose. During development, the slug becomes enveloped within an extracellular,
cellulose-based slime sheath and later, during terminal fruiting body formation, each cell
acquires its own cellulose-based cell wall. The cellulose is predominantly microfibrillar and
assembled via the action of a single CAZy GT2 family synthase [129] that is highly conserved
between D. discoideum and D. purpureum. Sheath and stalk cell walls are invested with distinct
classes of small proteins (sheathins) containing or consisting exclusively of cellulose-binding
CBDs [130]. Both classes are represented as large multigene families of up to 36 members
(Table S16). The spore coat is specialized by the presence of the Gal/GalNAc-rich
polysaccharide and 2 diglycosyltransferase genes required for its formation [131] are also
conserved in D. purpureum. The D. discoideum spore coat also contains at least 8 major coat
proteins, two of which have cellulose-binding activity in vitro [132]. D. purpureum orthologs are
found for six and are evidently evolving more rapidly than most proteins, as their amino acid
sequences are only ~61% similar and 48% identical, and half exhibit additional or alternative
Cys-rich domains.
81
Table S16. Genes of the Dictyostelid glycome (gene number differences in orange).
CAZy Family
GT family1
1
2
3
4
5
8
10
13
14
17
20
22
24
33
35
39
41
49
50
57
58
59
60
66
74
76
77
other
other
other
other
Total
GH family2
2
3
5
7
9
13
15
16
18
20
22
23
24
25
D. purpureum
3
9
1
7
1
2
6
2
3
0
2
3
1
1
2
1
2
2
1
3
2
1
2
1
1
1
1
1
1
1
2
66
D. discoideum
D. purpureum
1
1
6
1
8
5
2
2
13
3
3
3
0
6
D. discoideum
4
9
1
7
1
1
11
2
3
4
3
3
1
1
2
1
1
4
1
2
2
1
2
1
1
1
1
1
1
1
9
83
1
1
5
1
8
5
2
2
7
5
5
0
2
6
82
Glycogene Class
Glycosyltransferases/glycophosphotransferases
UGT small molecule
cytoplasmic inverting
glycogen synthase
E7E retaining
starch or 3glucan synthase
retaining, secretory
3/4FucT
Gnt1 (N-glycan); POMGnt1
Core2, XylT, I-branch 6GlcNAcT
bisect/intersect GlcNAcT
trehalose-PO4 synthase
alg9, alg12, ManT (GPI)
Parodi enzyme
4ManT, alg1
glycogen phosphorylase
prot O-ManT
Spy OGT
3GlcNAcT
pigM (GPI 4ManT-I)
GlcT
alg3
2GlcT for N-glycan prec
gnt1 (Skp1), gnt2 (modB)
stt3 (oligosaccharyltransferase)
pgtA (2FucT for Skp1)
6ManT (pigV GPI)
agtA (Skp1)
GT10/23-like, 3/6-FucT-like
alg7 (GlcNAc-PO4-T to Dol-P)
GlcNAc-PO4-T (Man-6-PO4)
glycophosphotransferase
Glycohydrolases
-glycosidase (potential endo--mannosidase)
-glycosidase (bacteria-type)
-glycosidase
reducing end cellobiohydrolase
cellulase
-amylase
trehalase, glucoamylase
polysaccharidase
chitinase
nagA -GlcNAcase
lysozyme C
lysozyme G
lysozyme
lysozyme
27
29
31
35
37
38
39
47
63
65
77
85
89
2
2
2
2
1
11
2
8
1
1
1
1
1
89
Total
CBM family2
D. purpureum
8
13
20
33
48
49
50
other
other
D. purpureum
13
2
15
D. discoideum
10
2
12
discoidin
comitin or comitin-like
D. purpureum
1
2
3
D. discoideum
Carbohydrate esterases
1
2
D. purpureum
7
D. discoideum
D. purpureum
6
D. discoideum
Total
CE family1
Spore coat3
Carbohydrate binding modules (appended to
enzyme domains)
Dictyostelium-specific cellulose binding (e.g.,
celA)
Cup (cytoplasmic)
glucoamylase, laforin
Dictyostelium- & bacteria-specific chitin-binding
glycogen-binding, AMPK
cellulose-binding, sheathins
binds chitin or peptidoglycan
4
10
5
3
3
45
4
74
CBD family3
Expansin-like2
D. discoideum
-galactosidase, -GalNAcase
-fucosidase
-glucosidase
-galactosidase
trehalase
manA (-mannosidase-II)
-glycosidase
-mannosidase-I
-glucosidase
trehalase, trehalose phosphorylase
4--glucanotransferase
endoglucosaminidase
-N-acetylglucosaminidase
3
3
5
3
3
39
7
63
Total
Total
2
2
2
2
1
7
3
6
1
1
1
1
1
80
Grand Total
249
1
2
3
Expansin-related proteins
7
Spore coat proteins
8
267
1
enumerated in Table S17
enumerated in Table S18
3
enumerated in Table S19.
2
83
Table S17. Glycosyltransferases/glycophosphotransferases and Carbohydrate esterases of
the Dictyostelids.
D. p.
Protein ID
D. p. dictyBase
Gene I.D.
Name
D. discoideum
Ortholog
Family
Predicted function
%
ident.
% target
(amino
acids)
Glycosyltransferases (GT Families)
74375
DPU_G0073034
DDB_G0278473
unassigned
95768
DPU_G0066680
ugt52
DDB_G0288655
GT Family 1
88818
DPU_G0058150
ugt1
DDB_G0290339
GT Family 1
35006
73885
146960
92136
35249
DPU_G0055140
DPU_G0051156
DPU_G0071316
DPU_G0054322
DPU_G0055570
ugt2
dcsA
dgtA
DDB_G0268540
DDB_G0289973
DDB_G0278817
DDB_G0269124
DDB_G0288321
GT Family 1
GT Family 2
GT Family 2
GT Family 2
GT Family 2
30502
DPU_G0072038
dgtB
DDB_G0286519
GT Family 2
47347
DPU_G0075876
pgtB
DDB_G0290079
56261
DPU_G0056760
pgtC
DDB_G0284107
87341
DPU_G0074572
pgtD
DDB_G0278731
GT Family
2; GT
Family 4
GT Family
2; GT
Family 4
GT Family
2; GT
Family 4
159362
DPU_G0070358
pgtA
DDB_G0283761
148003
45300
DPU_G0058290
DPU_G0058250
glcS
alg11
DDB_G0267674
DDB_G0292118
GT Family
2; GT
Family 74
GT Family 3
GT Family 4
88372
DPU_G0055520
alg2
DDB_G0272730
GT Family 4
42846
DPU_G0069094
gtr1
DDB_G0274373
GT Family 4
148633
DPU_G0063480
pigA
DDB_G0283965
GT Family 4
158449
DPU_G0067810
gtr2
DDB_G0276105
GT Family 5
86718
154205
57337
DPU_G0068020
DPU_G0057064
DPU_G0061546
gtr3
DDB_G0286945
fut10
DDB_G0286889
156375
DPU_G0062344
fut9
DDB_G0293768
157080
DPU_G0064180
fut7
DDB_G0283287
GT Family 8
GT Family 8
GT Family
10
GT Family
10
GT Family
10
84
distantly related to
fucosyltransferases
UDP-Glc: sterol
glucosyltransferase
distantly related to GTs
related to -GTs
candidate -GT
candidate -GT
cellulose synthase
candidate dolicholphosphate glucosyltransferase
candidate GDP-Man:
Dol-phosphate mannosyltransferase
bifunctional -GT/GT
34
77(543)
58
100(1756)
63
99(398)
46
43
62
88
77
100(440)
84(490)
97(612)
100(1067)
100(327)
82
99(251)
66
99(1343)
bifunctional -GT/GT
48
94(1029)
candidate
multimodular
bifunctional -GT/GT
bifunctional -1,3GalT/-1,2-fucT
55
96(2185)
57
99(771)
glycogen synthase
-1,2mannosyltransferase
-1,3mannosyltransferase
candidate
bifunctional
GT/sulfotransferase
UDP-GlcNAc:
phosphatidylinositol
-1,6-GlcNAcT
candidate
bifunctional protein:
distantly related to
amylases and
glycogen synthases
candidate -GT
related to -GTs
candidate 3/4-FucT
69
75
100(894)
95(479)
73
99(417)
60
100(1321)
93
88(460)
67
99(2500)
62
99(367)
51
97(644)
candidate 3/4-FucT
56
100(560)
candidate 3/4-FucT
57
88(435)
6690
DPU_G0064160
fut4
DDB_G0284551
GT Family
10
GT Family
10
80087
DPU_G0055858
fut8
DDB_G0280571
27418
DPU_G0058850
fut11
DDB_G0268190
88972
DPU_G0059144
gnt3
DDB_G0288463
91685
DPU_G0072472
gnt4
DDB_G0268854
GT Family
13
93669
DPU_G0059368
gnt10
DDB_G0269900
GT Family
14
96706
DPU_G0060270
gnt11
DDB_G0269558
GT Family
14
149262
DPU_G0067706
gnt9
DDB_G0268204
GT Family
14
46972
DPU_G0074060
tpsB
DDB_G0284975
GT Family
20
47494
DPU_G0051860
tpsC
DDB_G0290405
GT Family
20
149392
DPU_G0068484
smp3
DDB_G0284459
GT Family
22
96848
DPU_G0063556
alg9
DDB_G0279349
80121
DPU_G0056042
alg12
DDB_G0267884
82586
DPU_G0063038
ggtA
DDB_G0274103
GT Family
22
GT Family
22
GT Family
24
52859
DPU_G0059326
alg1
DDB_G0286011
GT Family
33
45567
DPU_G0061194
glpD
DDB_G0291123
51433
DPU_G0070164
glpV
DDB_G0281383
99420
DPU_G0065082
pmtA
DDB_G0284847
39606
DPU_G0062462
spyA
DDB_G0285263
151710
DPU_G0051722
spyB
51901
DPU_G0073636
gnt13
DDB_G0282469
152182
DPU_G0052592
gnt15
DDB_G0274741
158484
DPU_G0067852
pigM
DDB_G0288899
GT Family
35
GT Family
35
GT Family
39
GT Family
41
GT Family
41
GT Family
49
GT Family
49
GT Family
50
GT Family
10
GT Family
13
85
candidate 3/4-FucT
potential N-acetyl-D-glucosaminide 1,6-FucT
candidate 3/4-FucT
49
92(589)
47
93(788)
candidate -1,2GlcNAcT, 2GnT1?
(complex)
related to -Nacetylglucosaminyltr
ansferases
candidate -1,6GlcNAcT or
polypeptide XylT
candidate -1,6GlcNAcT or
polypeptide XylT
candidate -1,6GlcNAcT or
polypeptide XylT
candidate ,trehalose-6phosphate
synthase/phosphatase
candidate ,trehalose-6phosphate
synthase/phosphatase
candidate Dol-PMan: -1,2mannosyltransferase
Dol-P-Man: -1,2mannosyltransferase
Dol-P-Man: -1,6mannosyltransferase
UDPglucose:glycoprotein
-glucosyltransferase
(Parodi enz.)
GDP-mannose -1,4mannosyltransferase
(mntA)
glycogen
phosphorylase
glycogen
phosphorylase
related to protein Omannosyltransferases
O-GlcNAcT,
cytoplasmic
O-GlcNAcT,
cytoplasmic
candidate -GT
46
98(490)
58
88(572)
27
78(644)
40
99(501)
40
65(419)
81
99(788)
70
100(897)
41
98(1231)
74
98(634)
44
98(633)
60
100(1714)
70
97(477)
84
99(993)
93
99(846)
82
100(211)
58
92(810)
45
84(536)
candidate -GT
48
85(440)
Dol-phosphatemannose -1,4-
83
98(431)
38502
DPU_G0060630
alg8
DDB_G0275261
43700
DPU_G0071234
alg6
DDB_G0283841
37084
DPU_G0058522
alg3
DDB_G0268238
153070
DPU_G0054568
pigB
DDB_G0279825
GT Family
58
85245
DPU_G0072078
alg10
DDB_G0277817
gnt2
DDB_G0291241
GT Family
59
GT Family
60
EST only
GT Family
57
GT Family
57
GT Family
58
89733
DPU_G0063838
gnt1
DDB_G0275699
GT Family
60
150543
DPU_G0073564
stt3
DDB_G0285159
98471
DPU_G0056892
pigV
DDB_G0280891
152231
DPU_G0052824
agtA
DDB_G0283005
GT Family
66
GT Family
76
GT Family
77
mannosyltransferase
Dol-P-Glc: -1,3GlcT2
Dol-P-Glc: -1,3GlcT1
Dol-P-Man: 1,2/1,3mannosyltransferase
related to Dol-PMan: -1,2mannosyltransferases
related to Dol-P-Glc:
-1,2-GlcT1
polypeptide GlcNAcT (mucintype)
UDP-GlcNAc:HyPro
Skp1 polypeptide GlcNAc-transferase
oligosaccharyltransfe
rase subunit STT3
Dol-P-Man: 6mannosyltransferase
UDP-Gal:fucoside 1,3galactosyltransferase
67
96(602)
72
99(525)
61
99(459)
47
98(1215)
56
46(265)
56
100(425)
90
100(714)
56
99(647)
62
99(642)
Predicted glycophosphotransferases
158811
DPU_G0068698
gpt1
DDB_G0285815
158821
DPU_G0068712
gpt5
DDB_G0274707
97408
DPU_G0073430
gpt10
DDB_G0281103
158539
DPU_G0068028
alg7
DDB_G0290751
N-glycan: GlcNAcPO4-transferase
glycophosphotransf
erase
glycophosphotransf
erase
Dol-P-dependent
GlcNAc-1-P
transferase (Nglycan)
54
candidate esterase,
lacks signal peptide
candidate esterase
candidate esterase,
lacks signal peptide
62
99(282)
66
64
99(363)
82(347)
49
82
Predicted carbohydrate esterases
74322
DPU_G0071384
27230
37730
DPU_G0057788
DPU_G0059526
esd
DDB_G0283037
CE Family 1
DDB_G0275371
DDB_G0287647
CE Family 2
CE Family 2
Table S18. glycohydrolase, carbohydrate binding module, and expansin-like domain
containing proteins of the Dictyostelids.
D. p.
Protein ID.
D. p. dictyBase
Gene I.D.
Name
D.d. Ortholog
Family
Predicted Function
%
ident.
% of target
(amino
acids)
Glycohydrolases
97798
DPU_G0051944
manH
DDB_G0275917
48170
DPU_G0054796
gluA
DDB_G0292810
91906
DPU_G0075826
52841
DPU_G0058880
DDB_G0286025
GH Family
02
GH Family
03
GH Family
05
GH Family
86
candidate mannosidase
candidate glucosidase
candidate glycosidase
candidate -
57
100(1056)
81
100(831)
79
96(537)
05
47102
DPU_G0074860
DDB_G0286061
GH Family
05
152047
DPU_G0052360
DDB_G0289953
148310
DPU_G0060794
DDB_G0270190
GH Family
05
GH Family
05
148335
DPU_G0060842
DDB_G0270074
GH Family
05
151874
DPU_G0051994
cbhA
DDB_G0268446
GH Family
07
39756
DPU_G0062978
celA
DDB_G0271134
87197
DPU_G0073568
DDB_G0284295
31382
DPU_G0074154
DDB_G0279995
40165
DPU_G0063752
DDB_G0284239
40261
DPU_G0063986
DDB_G0286321
85868
DPU_G0074378
DDB_G0271314
36716
DPU_G0057932
DDB_G0286277
GH Family
09
GH Family
09
GH Family
09
GH Family
09
GH Family
09
GH Family
09
GH Family
09
153014
DPU_G0054480
50145
DPU_G0063042
glgB
DDB_G0274105
GH Family
13
45888
DPU_G0065672
agl
DDB_G0287569
GH Family
13
55676
DPU_G0054822
amyA
DDB_G0281547
87665
DPU_G0051736
amyB
DDB_G0286079
55969
DPU_G0055704
amyC
DDB_G0282715
33519
DPU_G0052964
DDB_G0277045
92511
DPU_G0059274
DDB_G0276215
149133
DPU_G0066922
DDB_G0280263
48687
DPU_G0056598
DDB_G0292848
GH Family
13
GH Family
13
GH Family
13
GH Family
15
GH Family
15
GH Family
16
GH Family
16
GH Family
09
87
glycosidase; CBM8
module; GPI
anchor, putative
cellulase
candidate glycosidase; CBM8
module; GPI-anchor
candidate
endoglucanase
candidate
endoglucanase;
CBM49 module,
putative cellulase
candidate
endoglycoceramidas
e
candidate [reducing
end] b-1,4cellobiohydrolase
endoglucanase,
CBM8 expected
candidate
endoglucanase
candidate
endoglucanase
candidate
endoglucanase
candidate
endoglucanase
candidate
endoglucanase
candidate
endoglucanase; GPI
anchor
candidate
endoglucanase; GPI
anchor
-1,4-glucan
branching enzyme ;
CBM48 module, amylase
glycogen
debranching
enzyme amylo-1,6-glucosidase
candidate amylase
candidate amylase
candidate trehalose
synthase, -amylase
candidate ,trehalase
candidate glycosidase
candidate endo1,3/4-glucanase
inactive glycosidase
(missing catalytic
61
100(547)
50
100(793)
66
96(551)
73
98(498)
80
99(453)
82
62(434)
83
90(434)
61
60(501)
74
66(449)
55
91(520)
76
100(454)
53
82(499)
84
100(675)
71
100(1608)
80
100(469)
88
96(495)
76
100(778)
77
83(545)
91
98(638)
66
89(244)
67
94(951)
50758
DPU_G0066176
DDB_G0268090
GH Family
18
GH Family
18
GH Family
18
GH Family
18
47033
DPU_G0074484
ctbsB
DDB_G0276795
156870
DPU_G0063718
ctbsA
DDB_G0274233
75595
DPU_G0061716
chid1
DDB_G0290417
85320
DPU_G0072384
93366
DPU_G0057482
DDB_G0278071
GH Family
18
75666
DPU_G0062690
DDB_G0287463
88230
DPU_G0054814
91849
DPU_G0075114
98002
DPU_G0053622
149996
DPU_G0071494
151171
DPU_G0075100
96643
DPU_G0058838
30528
DPU_G0072046
nagA
DDB_G0287033
83242
DPU_G0064898
nagE
DDB_G0285647
93851
DPU_G0065710
nagD
DDB_G0287659
41144
DPU_G0065448
lysB
DDB_G0278563
GH Family
18
GH Family
18
GH Family
18
GH Family
18
GH Family
18
GH Family
18
GH Family
18
GH Family
20
GH Family
20
GH Family
20
GH Family
22
151645
DPU_G0051586
156720
DPU_G0063338
147060
DPU_G0073036
153079
DPU_G0054584
153511
DPU_G0055578
20023
DPU_G0055886
cf45-1
DDB_G0269248
31893
DPU_G0075018
cf50-1
DDB_G0273175
39207
DPU_G0061924
GH Family
18
DDB_G0287465
rcdBB
DDB_G0288143
GH Family
22
DDB_G0274551
GH Family
22
GH Family
23
DDB_G0293566
GH Family
23
GH Family
23
GH Family
25
GH Family
25
GH Family
25
88
residues)
candidate chitinase
candidate di-Nacetylchitobiase
di-Nacetylchitobiase
inactive chitinase
(missing catalytic
residues), chitinase
domain-containing
protein 1
candidate inactive
chitinase (missing
catalytic residues)
candidate inactive
chitinase (missing
catalytic residues)
related to chitinases
63
97(252)
58
99(374)
58
97(372)
51
99(388)
33
90(292)
25
73(331)
42
83(383)
73
100(533)
44
94(663)
46
92(563)
75
94(190)
36
57(111)
41
100(339)
61
99(297)
62
99(302)
58
100(217)
related to chitinases
related to chitinases
related to chitinases
related to chitinases
related to chitinases
related to chitinases
N-acetyl glucosaminidase
related to N-acetyl
-glucosaminidase
related to N-acetyl
-glucosaminidase
distantly related to
lysozymes,
lysozyme C family
distantly related to
lysozymes,
lysozyme C family
distantly related to
lysozymes
distantly related to
lysozymes, similar
to lysozyme C
distantly related to
lysozymes
distantly related to
lysozymes
distantly related to
lysozymes, counting
factor complex
protein
distantly related to
lysozymes
distantly related to
lysozymes
81570
DPU_G0060048
DDB_G0274181
88463
DPU_G0055994
DDB_G0293492
154665
DPU_G0058236
DDB_G0276439
58841
DPU_G0069506
DDB_G0291524
86485
DPU_G0064266
DDB_G0294140
58554
DPU_G0067796
alfB
DDB_G0276661
88361
DPU_G0055470
alfA
DDB_G0274391
49160
DPU_G0058762
modA
DDB_G0269154
157944
DPU_G0066330
gaa
DDB_G0269790
157172
DPU_G0064456
glb1
DDB_G0290217
48969
DPU_G0058132
glb2
DDB_G0285637
41704
DPU_G0066730
49593
DPU_G0060478
manA
DDB_G0292206
55378
DPU_G0053628
manG
DDB_G0287577
34840
DPU_G0054962
manB
DDB_G0278259
47917
DPU_G0053730
manF
DDB_G0287231
98237
DPU_G0055394
manC
DDB_G0268994
40536
DPU_G0064404
manD
DDB_G0278653
45100
DPU_G0054176
manE
DDB_G0278651
48877
DPU_G0057412
manI
GH Family
38
96508
DPU_G0054174
manJ
GH Family
38
99980
DPU_G0070820
manK
GH Family
38
74852
DPU_G0054178
manL
GH Family
38
DDB_G0283473
GH Family
25
GH Family
25
GH Family
25
GH Family
27
GH Family
27
GH Family
29
GH Family
29
GH Family
31
GH Family
31
GH Family
35
GH Family
35
GH Family
37
GH Family
38
GH Family
38
GH Family
38
GH Family
38
GH Family
38
GH Family
38
GH Family
38
89
distantly related to
lysozymes
distantly related to
lysozymes
distantly related to
lysozymes
candidate galactosidase, or
alpha-Nacetylgalactosamini
dase
candidate galactosidase
-L-fucosidase
62
100(215)
65
100(215)
68
84(393)
74
99(384)
62
99(456)
-L-fucosidase
65
99(459)
 glucosidase II
75
99(938)
candidate glucosidase
candidate galactosidase
candidate galactosidase
candidate ,trehalase
candidate mannosidase
candidate mannosidase
related to mannosidases
related to mannosidases
related to mannosidases
related to mannosidases; Cterminal membrane
anchor
related to mannosidases; Cterminal membrane
anchor
related to mannosidases; Cterminal membrane
anchor
related to mannosidases; Cterminal membrane
anchor
related to mannosidases; Cterminal membrane
anchor
related to mannosidases; Nand C-terminal
78
100(867)
64
94(637)
57
99(757)
69
92(548)
70
100(1008)
67
99(1082)
63
100(1043)
59
100(994)
55
99(1074)
42
98(1212)
44
78(1112)
78906
DPU_G0052928
DDB_G0281313
GH Family
39
11305
DPU_G0053732
DDB_G0288289
55071
DPU_G0052284
msdA
DDB_G0268754
GH Family
39
GH Family
47
86464
DPU_G0063912
msdB
DDB_G0284391
GH Family
47
155265
DPU_G0059682
msdC
DDB_G0284395
GH Family
47
157585
DPU_G0065480
msdD
DDB_G0292918
GH Family
47
91147
DPU_G0052066
msdE
DDB_G0277051
GH Family
47
74722
DPU_G0052784
msdG
147471
DPU_G0052790
msdF
28384
DPU_G0063916
msdH
53711
DPU_G0069350
97948
DPU_G0053166
46840
DPU_G0073540
DDB_G0284259
95866
DPU_G0067914
DDB_G0268520
GH Family
85
26247
DPU_G0052098
DDB_G0291998
GH Family
89
DDB_G0277757
CBM
Family 08
DDB_G0284393
DDB_G0280145
athl1
naglu
DDB_G0287109
GH Family
47
GH Family
47
GH Family
47
GH Family
63
GH Family
65
GH Family
77
membrane anchor
candidate glycosidase; Cterminal membrane
anchor
candidate xylosidase
mannosyloligosaccharide
a1,2-mannosidase
mannosyloligosaccharide
1,2-mannosidase
mannosyloligosaccharide
1,2-mannosidase;
N-terminal
membrane anchor
mannosyloligosaccharide
1,2-mannosidase;
N-terminal
membrane anchor
mannosyloligosaccharide
1,2-mannosidase
related to mannosidases
mannosyloligosaccharide
1,2-mannosidase
too short to be
reliably annotated
Mannosyloligosaccharide
glucosidase
acid trehalase-like
protein 1
candidate 4-glucanotransferase;
two N-terminal
CBM20 modules
related to endo--Nacetylglucosaminida
ses
related to -Nacetylglucosaminida
ses
49
83
59
75(493)
54
75(441)
45
95(615)
51
89(511)
47
100(796)
55
38(192)
54
99(878)
55
100(679)
84
100(909)
41
100(1362)
70
89(725)
57
97(368)
Carbohydrate binding modules
95208
DPU_G0059732
76197
DPU_G0066892
cupK
CBM
Family 13
158837
DPU_G0068828
cupL
CBM
Family 13
90
candidate
carbohydratebinding protein
carbohydratebinding protein,
ricin B lectin
domain-containing
protein
carbohydratebinding protein,
ricin B lectin
15974
DPU_G0072456
149039
cupI
DDB_G0272242
CBM
Family 13
DPU_G0066074
DDB_G0270014
CBM
Family 20
58838
DPU_G0069496
DDB_G0272062
CBM
Family 20
35223
DPU_G0055550
DDB_G0290085
CBM
Family 20
53299
DPU_G0064966
DDB_G0273103
CBM
Family 33
55507
DPU_G0054064
DDB_G0273835
CBM
Family 33
79382
DPU_G0054062
DDB_G0277201
CBM
Family 33
99095
DPU_G0062228
DDB_G0269710
CBM
Family 48
74639
DPU_G0052060
ptdC
149760
DPU_G0070402
ptdA
DDB_G0281079
26246
DPU_G0052058
ptdB
DDB_G0281077
33217
DPU_G0052432
57109
DPU_G0060486
ecmG
DDB_G0292224
78730
DPU_G0052390
ecmL
DDB_G0293762
78747
DPU_G0052430
ecmM
93241
DPU_G0070896
ecmF
152083
DPU_G0052428
ecmN
154318
DPU_G0057266
celB
DDB_G0269112
157586
DPU_G0065482
ecmD
DDB_G0286647
56144
DPU_G0056304
staA
DDB_G0294473
CBM
Family 49
CBM
Family 49
CBM
Family 49
DDB_G0287275
CBM
Family 49
CBM
Family 49
CBM
Family 49
CBM
Family 49
CBM
Family 49
DDB_G0291291
CBM
Family 49
CBM
Family 49
CBM
Family 49
CBM
Family 49
91
domain-containing
protein
carbohydratebinding protein,
ricin B lectin
domain-containing
protein
candidate
carbohydratebinding protein
candidate
carbohydratebinding protein
candidate
multimodular
carbohydratebinding protein
candidate
carbohydratebinding protein
candidate
carbohydratebinding protein
candidate
carbohydratebinding protein
candidate
carbohydratebinding protein
candidate peptidase
C1A; sheathin-like
candidate peptidase
C1A; sheathin-like
candidate peptidase
C1A; two CBM49
modules; C-terminal
membrane anchor
sheathin-like
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
34
87(620)
79
92(190)
73
100(148)
63
100(1590)
62
97(233)
45
96(241)
36
91(233)
51
100(1495)
(566)
32
97(642)
40
93(740)
28
50(692)
58
94(117)
43
98(1124)
sheathin-like
(1118)
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
49
sheathin-like
46
80(103)
(1137)
96(519)
sheathin
(271)
sheathin-like,
sheathin-like
domains may be
solitary
(152)
57657
DPU_G0063026
CBM
Family 49
150550
DPU_G0073576
CBM
Family 49
91080
DPU_G0071334
CBM
Family 49
77419
DPU_G0073538
CBM
Family 49
94401
DPU_G0075866
CBM
Family 49
156962
DPU_G0063962
CBM
Family 49
22202
DPU_G0058510
CBM
Family 49
50740
DPU_G0066108
CBM
Family 49
153444
DPU_G0055454
CBM
Family 49
98184
DPU_G0054972
CBM
Family 49
91241
DPU_G0056960
35222
DPU_G0055556
CBM
Family 49
CBM
Family 49
78284
DPU_G0075864
CBM
Family 49
148310
DPU_G0060794
79711
DPU_G0054974
CBM
Family 49
CBM
Family 49
91957
DPU_G0051890
97652
DPU_G0075514
40477
DPU_G0064212
CBM
Family 49
CBM
Family 49
CBM
92
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
(271)
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
(164)
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
(152)
sheathin-like
(476)
sheathin-like,
(151)
(155)
(152)
(138)
(140)
(150)
(125)
(152)
(152)
(151)
(198)
(164)
(560)
(372)
Family 49
12263
DPU_G0061576
CBM
Family 49
149279
DPU_G0067738
CBM
Family 49
154567
DPU_G0058060
36696
DPU_G0057944
CBM
Family 49
CBM
Family 49
93076
DPU_G0067812
CBM
Family 49
73532
DPU_G0067806
CBM
Family 49
158052
DPU_G0066778
83697
DPU_G0066272
CBM
Family 49
CBM
Family 49
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
(151)
(151)
(321)
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like,
sheathin-like
domains may be
solitary
sheathin-like
(151)
sheathin-like,
sheathin-like
domains may be
solitary
(123)
(151)
(151)
(619)
Cell Wall Expansins
155955
DPU_G0061384
expl1
DDB_G0267846
EXPN
148118
DPU_G0059332
expl5
DDB_G0276937
EXPN
20287
DPU_G0054872
expl3
DDB_G0276287
EXPN
55762
DPU_G0055032
expl2
DDB_G0284677
EXPN
92439
DPU_G0058204
expl10
DDB_G0284549
EXPN
37473
DPU_G0059154
expl11
88764
DPU_G0057922
expl12
EXPN
DDB_G0284479
EXPN
distantly related to
plant expansins
distantly related to
plant expansins
distantly related to
plant expansins; Cterminal membrane
anchor
distantly related to
plant expansins; Cterminal membrane
anchor
distantly related to
plant expansins;
three CBM50
modules
distantly related to
plant expansins; two
CBM50 modules
distantly related to
plant expansins; two
CBM50 modules
53
86(246)
70
99(236)
73
68(229)
76
98(402)
52
93(277)
53
100(270)
Table S19. Proposed carbohydrate-binding-domain containing and spore coat proteins of
the Dictyostelids.
93
D.p.
D. p. dictyBase
Protein
Gene I.D.
I.D.
Comitin-related proteins
Name
D.d. Ortholog
Predicted Function
75958
DPU_G0064986
38686
DPU_G0061038
Spore coat-related proteins
cmr
comA
DDB_G0279711
DDB_G0289599
comitin-like protein, 134 aa in Dd
comitin, 185 aa in Dd
97410
96596
92698
92740
DPU_G0073446
DPU_G0057732
DPU_G0061834
DPU_G0062794
cotA
cotB
cotD
pspB
DDB_G0276941
DDB_G0276761
DDB_G0283149
DDB_G0276939
99604
150519
DPU_G0066804
DPU_G0073470
pspD
psvA
DDB_G0277379
DDB_G0276869
SP96, 600 aa in Dd
SP70, 537 aa in Dd
SP75, 554 aa in Dd
SP85, cellulose-binding, 532 aa in
Dd
SP87, 677 aa in Dd
p58/SP35, cellulose-binding, 513 aa
in Dd
dscA1
DDB_G0273063
%
ident.
% of target
(amino
acids)
(135)
(201)
57
34
53
39
(489)
(517)
(598)
(603)
72
61
(515)
(565)
Discoidin-related proteins
52865
DPU_G0059342
160079
DPU_G0072822
91146
DPU_G0052050
146689
DPU_G0062490
75318
DPU_G0059346
152743
DPU_G0053890
57504
DPU_G0062294
58954
DPU_G0070126
56540
DPU_G0058448
91250
DPU_G0057764
93835
DPU_G0065018
156718
DPU_G0063334
52224
DPU_G0072994
Sheathin-like proteins
discoidin
(255)
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
discoidin
(255)
(255)
(255)
(257)
(256)
(253)
(253)
(252)
(253)
(253)
(254)
(278)
see CAZy family CBM 49 carbohydrate binding module entries in Table S18 above.
Cup-like proteins
see CAZy family CBM 13 carbohydrate binding module entries in Table S18 above.
Social Genes
Analysis of social genes
We used 12,410 predicted coding sequences and protein sequences of Dictyostelium
purpureum along with 13,349 of Dictyostelium discoideum retrieved from dictyBase (version of
10/25/2009 [14]). Illumina RNA-seq reads from cDNA libraries of the vegetative stage and six
social stages at four-hour intervals of 12,713 D. discoiduem genes and 12,246 D. purpureum
genes were obtained by personal communication [15].
94
We constructed a social expression index for each gene to describe its relative expression
in social versus vegetative stages, for genes with > 30 RNA-seq reads at least in one time point
of development and high reproducibility between biological replicates (> 0.9 Pearson’s
correlation between expression profiles from the two biological replicates) in D. discoideum
(3,039 genes) and D. purpureum (5,751 genes). The number of reads per gene was normalized
for each time point and then averaged over all social time points to give average social
expression. The social expression index is defined as this social average divided by the social
average plus the normalized vegetative count. We also constructed gamete expression indices for
genes with at least four RNA-seq ESTs expressed in the vegetative and gamete stages from D.
discoideum (932 genes).
Comparative analyses of social genes used relatively strict orthology requirements to
avoid analyzing false matches. We applied Inparanoid 2.0 [116] for searching orthologs and inparalogs among protein sequences with at least 50 amino acid residues of D. purpureum and D.
discoideum, with parameter settings as follows: score cutoff = 100, out-group cutoff = 50,
sequence overlap cutoff = 0.8, confident cutoff = 0.05, group overlap cutoff = 0.5, grey zone = 0,
and bootstrap estimation of the confidence. To reduce false positive results caused by biased
amino acid usage (due to the very A+T content of the genomes), we adjusted the substitution
matrix BLOSUM62 based on amino acid compositions of the two species by using Yu's method
of composition-specific substitution matrix adjustment [133]. Our conservative procedure
yielded 5,504 D. purpureum genes being orthologous counterparts of 5,613 D. discoideum genes,
from which 5,651 (including 5,334 one-to-one orthologs) pairs of orthologs were constructed.
Thus, we analyzed orthologs for fewer than half of the genes, consistent with the large distance
95
between these two species. 232 and 447 orthologs had paralogs in D. purpureum and D.
discoideum, respectively.
Global sequence alignment of the orthologous genes was implemented by using the
program GAP4, which uses a dynamic alignment algorithm to improve sensitivity and
recognition of homologous regions from sequences with intermittent similarity [134]. Amino
acid substitution matrices BLOSUM45, BLOSUM62 and BLOSUM100 addressed by GAP4
were again adjusted based on the amino acid composition of D. purpureum and D. discoideum.
The alignments of protein sequences were subsequently retro-translated into DNA sequence
alignments for dN and dS calculation.
Degrees of divergence were measured by rates of non-synonymous change (dN), rates of
synonymous change (dS), and conservation score (CS). The value of dN and dS were calculated
by using a maximum likelihood method that was implemented by the program codeml of
PAML4 [135], with parameter settings as following: runmode = -2, CodonFreq = 1, model = 0,
NSsites = 0, icode = 0, Mgene = 0, ncatG = 10, and other parameters are defaults. The
conservation score is calculated by dividing the GAP4 similarly score of a protein to its ortholog
by the similarity score of the protein to itself [136].
96
Figure S18. Cheater genes and other genes do not differ in several measures of
evolutionary rates. A. Percentage with orthologs, |z| = 0.0885, p = 0.929. B. Percentage of orthologs
that have inparalogs, |z| = 0.262, p = 0.793. C. Non-synonymous substitution rate, |t| = 1.2454, df =
85.78, p = 0.216. The ratio of non-synonymous to synonymous change (dN/dS) often provides a more
sensitive measure of adaptive change, but the large distance between D. discoideum and D. purpureum
means that synonymous changes have saturated and are impossible to estimate accurately. D.
Conservation score, |t| = 0.8178, df = 86.64, p = 0.416. All tests are two-tailed.
97
Figure S19. Social expression index for both D. discoideum (A and C) and D. purpureum (B
and D) depending on whether the genes have orthologs (A and B), or inparalogs (C and D).
Boxes show quartiles, whiskers show the most extreme data point that is no more than 1.5 times the
interquartile range from the box, and circles show the outliers. Mann-Whitney U tests are used
throughout. Panel A. Genes without orthologs have higher social expression in D. discoideum than those
with orthologs, p < 0.0001. Panel B. Genes without orthologs also have higher social expression in D.
purpureum than those with orthologs, p < 0.0001. Panel C. Genes with inparalogs have no significantly
different social expression in D. discoideum from those without inparalogs, p = 0. 93. Panel D. Genes
with inparalogs have no significantly different social expression in D. purpureum from those without
inparalogs, p = 0.24.
98
Figure S20. Percentage of RNA-seq reads in different social stage as a function of
conservation score and non-synonymous substitution rate (dN) in D. discoideum (A) and D.
purpureum (B). A separate social expression index was calculated for each social time point against the
vegetative stage (hr00). Social expression index values and regression lines of stage hr04~hr24 were
marked in blue, red, green, lightblue, pink and yellow, respectively. Panel A. Using D. discoideum RNAseqs (1,739 genes), all the regressions on CS are significant (R2 = 0.036~0.061, p < 0.0001), as well as
most of the regressions on dN (R2 = 0.0098~0.020, p < 0.0001). Panel B. Using D. purpureum RNA-seqs,
(3,649 genes), all the regressions on CS are significant (R2 = 0.024~0.063, p < 0.0001), as well as all the
regressions on dN (R2 = 0.0012~0.012, p < 0.0001).
99
Figure S21. Comparison between meiotic genes and other genes in non-synonymous
substitution rate (A) and conservation score (B). The meiotic genes are Mlh1, Msh2, Msh6, Pds5,
Pms1, Rad18, Rad23, Rad50, Rad51, Scc3, Smc2, Smc3, and Smc4. Panel A. Non-synonymous
substitution rate, |t| = 0.20, df = 12.10, p = 0.85. Panel B. Conservation score, |t| = 0.78, df = 12.08, p =
0.45. Two tailed t-test.
100